Yeast expressing cellulases for simultaneous saccharification and fermentation using cellulose

ABSTRACT

The present invention is directed to cellulytic host cells. The host cells of the invention expressing heterologous cellulases and are able to produce ethanol from cellulose. According to the invention, host cells expressing a combination of heterologous cellulases can be used to produce ethanol from cellulose. In addition, multiple host cells expressing different heterlogous cellulases can be co-cultured together and used to produce ethanol from cellulose. Furthermore, the invention demonstrates for the first time the ability of  Kluveryomyces  to produce ethanol from cellulose. The yeast strains and co-cultures of yeast strains of the invention can be used to produce ethanol on their own, or can also be used in combination with externally added cellulases to increase the efficiency of saccharification and fermentation processes.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.13/130,549, filed Feb. 7, 2012, which is a '371 National StageApplication of International Application No. PCT/US2009/065571, filedNov. 23, 2009, which claims the benefit of U.S. Provisional ApplicationNo. 61/116,981, filed Nov. 21, 2008. The entire contents of eachapplication are incorporated herein by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Sep. 23, 2015, isnamed 191SeqList.txt and is 169,788 bytes in size.

BACKGROUND OF THE INVENTION

Lignocellulosic biomass is widely recognized as a promising source ofraw material for production of renewable fuels and chemicals. Theprimary obstacle impeding the more widespread production of energy frombiomass feedstocks is the general absence of low-cost technology forovercoming the recalcitrance of these materials to conversion intouseful fuels. Lignocellulosic biomass contains carbohydrate fractions(e.g., cellulose and hemicellulose) that can be converted into ethanol.In order to convert these fractions, the cellulose and hemicellulosemust ultimately be converted or hydrolyzed into monosaccharides; it isthe hydrolysis that has historically proven to be problematic.

Biologically mediated processes are promising for energy conversion, inparticular for the conversion of lignocellulosic biomass into fuels.Biomass processing schemes involving enzymatic or microbial hydrolysiscommonly involve four biologically mediated transformations: (1) theproduction of saccharolytic enzymes (cellulases and hemicellulases); (2)the hydrolysis of carbohydrate components present in pretreated biomassto sugars; (3) the fermentation of hexose sugars (e.g., glucose,mannose, and galactose); and (4) the fermentation of pentose sugars(e.g., xylose and arabinose). These four transformations occur in asingle step in a process configuration called consolidated bioprocessing(CBP), which is distinguished from other less highly integratedconfigurations in that it does not involve a dedicated process step forcellulase and/or hemicellulase production.

CBP offers the potential for lower cost and higher efficiency thanprocesses featuring dedicated cellulase production. The benefits resultin part from avoided capital costs, substrate and other raw materials,and utilities associated with cellulase production. In addition, severalfactors support the realization of higher rates of hydrolysis, and hencereduced reactor volume and capital investment using CBP, includingenzyme-microbe synergy and the use of thermophilic organisms and/orcomplexed cellulase systems. Moreover, cellulose-adherent cellulolyticmicroorganisms are likely to compete successfully for products ofcellulose hydrolysis with non-adhered microbes, e.g., contaminants,which could increase the stability of industrial processes based onmicrobial cellulose utilization. Progress in developing CBP-enablingmicroorganisms is being made through two strategies: engineeringnaturally occurring cellulolytic microorganisms to improveproduct-related properties, such as yield and titer, and engineeringnon-cellulolytic organisms that exhibit high product yields and titersto express a heterologous cellulase and hemicellulase system enablingcellulose and hemicellulose utilization.

Three major types of enzymatic activities are required for nativecellulose degradation: The first type are endoglucanases (1,4-β-D-glucan4-glucanohydrolases; EC 3.2.1.4). Endoglucanases cut at random in thecellulose polysaccharide chain of amorphous cellulose, generatingoligosaccharides of varying lengths and consequently new chain ends. Thesecond type are exoglucanases, including cellodextrinases(1,4-β-D-glucan glucanohydrolases; EC 3.2.1.74) and cellobiohydrolases(1,4-β-D-glucan cellobiohydrolases; EC 3.2.1.91). Exoglucanases act in aprocessive manner on the reducing or non-reducing ends of cellulosepolysaccharide chains, liberating either glucose (glucanohydrolases) orcellobiose (cellobiohydrolase) as major products. Exoglucanases can alsoact on microcrystalline cellulose, presumably peeling cellulose chainsfrom the microcrystalline structure. The third type are β-glucosidasesβ-glucoside glucohydrolases; EC 3.2.1.21). β-Glucosidases hydrolyzesoluble cellodextrins and cellobiose to glucose units.

Bakers' yeast (Saccharomyces cerevisiae) remains the preferredmicro-organism for the production of ethanol (Hahn-Hagerdal, B., et al.,Adv. Biochem. Eng. Biotechnol. 73, 53-84 (2001)). Favorable attributesof this microbe include (i) high productivity at close to theoreticalyields (0.51 g ethanol produced/g glucose used), (ii) high osmo- andethanol tolerance, (iii) natural robustness in industrial processes, and(iv) being generally regarded as safe (GRAS) due to its long associationwith wine and bread making, and beer brewing. Furthermore, S. cerevisiaeexhibits tolerance to inhibitors commonly found in hydrolyzatesresulting from biomass pretreatment.

One major shortcoming of S. cerevisiae is its inability to utilizecomplex polysaccharides such as cellulose, or its break-down products,such as cellobiose and cellodextrins. In attempt to address thisproblem, several heterologous cellulases from bacterial and fungalsources have been transferred to S. cerevisiae, enabling the degradationof cellulosic derivatives (Van Rensburg, P., et al., Yeast 14, 67-76(1998)), or growth on cellobiose (Van Rooyen, R., et al., J. Biotech.120, 284-295 (2005)); McBride, J. E., et al., Enzyme Microb. Techol. 37,93-101 (2005)). However, current levels of expression and specificactivity of cellulases heterologously expressed in yeast are still notsufficient to enable efficient growth and ethanol production by yeast oncellulosic substrates without externally added enzymes. There remains asignificant need for improvement in the amount of cellulase activity inorder to attain the goal of achieving a consolidated bioprocessing (CBP)system capable of efficiently and cost-effectively converting cellulosicsubstrates to ethanol.

Another major shortcoming of the use of S. cerevisiae is that externallyproduced cellulases function optimally at a higher temperature than thetemperature at which S. cerevisiae function optimally. Thus, either theprocessing must be carried out in a two step process at two differenttemperatures or one temperature can be selected where both processesfunction to some extent, but at least one of the processes does notoccur at optimal efficiency.

In order to address these limitations, the present invention providesfor heterologous expression of wild-type and codon-optimizedcombinations of heterologous cellulases in yeast that allows efficientproduction of ethanol from cellulose sources. The invention alsoprovides for expression of such heterologous cellulases intheromtolerant yeast and methods of using such transformed yeast forethanol production.

BRIEF DESCRIPTION OF THE INVENTION

The present invention is directed to cellulytic host cells. The hostcells of the invention expressing heterologous cellulases and are ableto produce ethanol from cellulose.

In particular, in some embodiments, the invention provides a transformedthermotolerant yeast host cell comprising at least one heterologouspolynucleotide comprising a nucleic acid encoding a cellulase, whereinthe yeast host cell is capable of producing ethanol when grown usingcellulose as a carbon source.

In another embodiment, the invention provides a transformedthermotolerant yeast host cell comprising: (a) at least one heterologouspolynucleotide comprising a nucleic acid which encodes an endoglucanase;(b) at least one heterologous polynucleotide comprising a nucleic acidwhich encodes a β-glucosidase; (c) at least one heterologouspolynucleotide comprising a nucleic acid which encodes a firstcellobiohydrolase; and (d) at least one heterologous polynucleotidecomprising a nucleic acid which encodes a second cellobiohydrolase.

In another embodiment, the invention provides a transformed yeast hostcell comprising: (a) at least one heterologous polynucleotide comprisinga nucleic acid which encodes a cellulase which is an endoglucanase; (b)at least one heterologous polynucleotide comprising a nucleic acid whichencodes a cellulase which is a β-glucosidase; (c) at least oneheterologous polynucleotide comprising a nucleic acid which encodes acellulase which is a first cellobiohydrolase; and (d) at least oneheterologous polynucleotide comprising a nucleic acid which encodes acellulase which is a second cellobiohydrolase, wherein at least two ofthe cellulases are secreted by the cell.

In yet another embodiment, the invention provides a transformed yeasthost cell comprising at least six heterologous polynucleotides, whereineach heterologous polynucleotide comprises a nucleic acid which encodesa cellulase.

In yet another embodiment, the invention provides a transformed yeasthost cell comprising at least four heterologous polynucloeotides,wherein each heterologous polynucleotide comprises a nucleic acid whichencodes an endogluconase.

In still another embodiment, the invention provides a co-culturecomprising at least two yeast host cells wherein (a) at least one of thehost cells comprises a first heterologous polynucleotide comprising anucleic acid which encodes a cellulase which is an endoglucanase; (b) atleast one of the host cells comprises a second heterologouspolynucleotide comprising a nucleic acid which encodes a cellulase whichis a β-glucosidase; (c) at least one of the host cells comprises a thirdheterologous polynucleotide comprising a nucleic acid which encodes acellulase which is a first cellobiohydrolase; (d) at least one of thehost cells comprises a fourth heterologous polynucleotide comprising anucleic acid which encodes a cellulase which is a secondcellobiohydrolase; wherein the first polynucleotide, the secondpolynucleotide, the third polynucleotide and the fourth polynucleotideare not in the same host cell; and wherein the co-culture is capable ofproducing ethanol from cellulose.

In some particular embodiments of the invention, the cellulose carbonsource is insoluble cellulose, crystalline cellulose, cellulose derivedfrom lignocellulose, hardwood, phosphoric acid swollen cellulose ormicrocrystalline cellulose.

In some embodiments, the host cells of the invention comprise aheterologous polynucleotide comprising a nucleic acid encoding a firstcellobiohydrolase, a polynucleotide comprising a nucleic acid encodingan endoglucanase, a polynucleotide comprising a nucleic acid encoding aβ-glucosidase and/or a polynucleotide comprising a nucleic acid encodinga second cellobiohydrolase.

In some embodiments, the cellulase, endoglucanase, β-glucosidase orcellobiohydrolase is a H. grisea, T. aurantiacus, T. emersonii, T.reesei, C. lacteus, C. formosanus, N. takasagoensis, C. acinaciformis,M. darwinensis, N. walkeri, S. fibuligera, C. lucknowense, R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, or Arabidopsis thaliana cellulase,endoglucanase, β-glucosidase or cellobiohydrolase.

In some particular embodiments, the cellobiohydrolase is an H. griseaCBH1, a T. aurantiacus CBH1, a T. emersonii CBH1, a T. reesei CBH1, a T.emersonii CBH2, a C. lucknowense CBH2 or a T. reesei CBH2. In someembodiments, the heterologous polynucleotide comprising a nucleic acidwhich encodes a cellobiohydrolase, encodes a fusion protein comprising acellobiohydrolase and a cellulose binding module (CBM). In someparticular embodiments, the CBM is the CBM of T. reesei CBH2, the CBM ofT. reesei CBH1 or the CBM of C. lucknowense CBH2b. In some particularembodiments, the CBM is fused to the cellobiohydrolase via a linkersequence. In some particular embodiments, the host cell expresses afirst and a second cellobiohydrolase, wherein the firstcellobiohydrolase is a T. emersonii CBH1 and CBD fusion, and the secondcellobiohydrolase is a C. lucknowense CBH2b.

In other particular embodiments, the β-glucosidase is a S. fibuligeraβ-glucosidase. In another particular embodiment, the endoglucanase is aC. formosanus endoglucanase. In another particular embodiment, theendoglucanse is a T. reesei endoglucanase, e.g. T. reesei EG2.

In some embodiments of the invention, at least one or at least two ofthe cellulases is tethered. In other embodiments of the invention, atleast one of the cellulases is secreted. In another embodiment, at leastone of the cellulases is tethered and at least one of the cellulases issecreted. In another embodiment, all of the cellulases are secreted.

In some embodiments of the invention, the nucleic acid encoding acellulase is codon optimized.

In some embodiments, the host cell can be a thermotolerant host cell. Insome embodiments, the host cell is a Issatchenkia orientalis, Pichiamississippiensis, Pichia mexicana, Pichia farinosa, Clavispora opuntiae,Clavispora lusitaniae, Candida mexicana, Hansenula polymorpha orKluveryomyces host cell. For example, in some embodiments, the host cellis a K. lactis or K. marxianus host cell. In some embodiments, thethermotolerant host cell is an S. cerevisiae host cell, wherein the S.cerevisiae is selected to be thermotolerant.

In some embodiments, the host cell can be an oleaginous yeast cell. Insome particular embodiments, the oleaginous yeast cell is a Blakeslea,Candida, Cryptococcus, Cunninghamella, Lipomyces, Mortierella, Mucor,Phycomces, Pythium, Rhodosporidium, Rhodotorula, Trichosporon orYarrowia cell.

In some embodiments, the host cell is a Saccharomyces cerevisiae cell.

In some particular embodiments, the host cell can produce ethanol fromcellulose at temperatures above about 30° C., 35° C., 37° C., 42° C.,45° C. or 50° C.

In another particular embodiment, the host cell can produce ethanol at arate of at least about 10 mg per hour per liter, at least about 30 mgper hour per liter, at least about 40 mg per hour per liter, at leastabout 50 mg per hour per liter, at least about 60 mg per hour per liter,at least about 70 mg per hour per liter, at least about 80 mg per hourper liter, at least about 90 mg per hour per liter, at least about 100mg per hour per liter, at least about 200 mg per hour per liter, atleast about 300 mg per hour per liter, at least about 400 mg per hourper liter, at least about 500 mg per hour per liter, at least about 600mg per hour per liter, at least about 700 mg per hour per liter, atleast about 800 mg per hour per liter, at least about 900 mg per hourper liter, or at least about 1 g per hour per liter.

The present invention also provides methods of using the host cells andco-cultures of the invention. For example, the present invention is alsodirected to a method for hydrolyzing a cellulosic substrate, comprisingcontacting said cellulosic substrate with a host cell or co-culture ofthe invention. The invention is also directed to a method of fermentingcellulose comprising culturing a host cell or co-culture of theinvention in medium that contains insoluble cellulose under suitableconditions for a period sufficient to allow saccharification andfermentation of the cellulose. In some particular embodiments, themethods further comprise contacting the cellulosic substrate withexternally produced cellulase enzymes.

In some particular methods of the invention, the cellulosic substrate isa lignocellulosic biomass selected from the group consisting of grass,switch grass, cord grass, rye grass, reed canary grass, miscanthus,sugar-processing residues, sugarcane bagasse, agricultural wastes, ricestraw, rice hulls, barley straw, corn cobs, cereal straw, wheat straw,canola straw, oat straw, oat hulls, corn fiber, stover, soybean stover,corn stover, forestry wastes, recycled wood pulp fiber, paper sludge,sawdust, hardwood, softwood, Agave, and combinations thereof.

In some particular methods of the invention, the host cell or co-cultureproduces ethanol. The ethanol can be produced at a rate of at leastabout 10 mg per hour per liter, at least about 30 mg per hour per liter,at least about 40 mg per hour per liter, at least about 50 mg per hourper liter, at least about 60 mg per hour per liter, at least about 70 mgper hour per liter, at least about 80 mg per hour per liter, at leastabout 90 mg per hour per liter, at least about 100 mg per hour perliter, at least about 200 mg per hour per liter, at least about 300 mgper hour per liter, at least about 400 mg per hour per liter, at leastabout 500 mg per hour per liter, at least about 600 mg per hour perliter, at least about 700 mg per hour per liter, at least about 800 mgper hour per liter, at least about 900 mg per hour per liter, or atleast about 1 g per hour per liter.

In other particular methods of the invention, the host cell orco-cultures contact a cellulosic substance at a temperature of at leastabout 37° C., least about 42° C., from about 42° C. to about 45° C., orfrom about 42° C. to about 50° C.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an image of a CMC plate assay to detect endoglucanase Iactivity in K. lactis (colonies numbered 1-8) and K. marxianus strains(colonies numbered 9-16) transformed with heterologous cellulases.Strains 8 and 16 are untransformed negative controls. The plate on theleft shows colony growth, and the plate on the right shows CMCaseactivity, indicated by the presence of a clearance zone. Clearance zonesappear as white spots in the image.

FIG. 2 depicts the results of an MU-lac assay to detect CBH1 activity inK. marxianus strains transformed with heterologous cellulases.

FIG. 3 depicts the percent of Avicel converted by several strains of K.marxianus expressing heterologous cellulases.

FIG. 4 depicts the ethanol production/consumption from Avicel by severalstrains of K. marxianus expressing heterologous cellulases.

FIG. 5 depicts the growth of S. cerevisiae expressing heterologouscellulases on bacterial microcrystalline cellulose (BMCC).

FIG. 6 depicts the ethanol production from Avicel by an S. cerevisiaestrain expressing heterologous cellulases.

FIG. 7 depicts the ethanol production from pretreated hardwood (5% basedon a dry weight percentage) by an S. cerevisiae strain expressingheterologous cellulases.

FIG. 8 depicts the ethanol production from pretreated hardwood (5% basedon a dry weight percentage) by an S. cerevisiae expressing heterologouscellulases in the presence of various concentrations of exogenouslyadded cellulases.

FIG. 9 depicts the ethanol production from Avicel by MO288 (circles) anda control strain (triangles) in both YP media and YNB media.

FIG. 10 depicts the ethanol yield from Avicel (15% based on a dry weightpercentage) by a small scale simultaneous saccharification andfermentation (SSF) process using S. cerevisiae supplemented withexternal cellulases. The yield from a yeast strain expressingheterologous cellulases (MO288) is compared to the yield from a controlstrain (MO249) at a variety of external cellulase concentrations over150 hours. (100% cellulase loading indicates 25 mg/g total solids;initial solids concentration was 15%.)

FIG. 11 depicts the theoretical ethanol yield from a simultaneoussaccharification and fermentation (SSF) process using S. cerevisiaesupplemented with external cellulases. The yield from a yeast strainexpressing heterologous cellulases (MO288) is compared to the yield froma control strain (MO249).

FIG. 12 illustrates the predicted cellulase enzyme savings based onethanol yield at 168 hours of simultaneous saccharification andfermentation (SSF) process.

FIG. 13 shows the activity of an artificial cellulase in the Avicelconversion assay as described in Example 9. The MO429 strain wastransformed the CBH1 consensus sequence “CBH1cons,” and the MO419 strainwas transformed with empty pMU451 vector as a negative control.Descriptions of other strains are found in Table 8 of Example 9.

FIG. 14 demonstrates the activity of yeast expressing variouscombinations of CBH1 and CBH2 enzymes on Avicel as described in Example10.

FIG. 15 demonstrates the activity of yeast expressing various cellulaseenzymes on Avicel as described in Example 10.

FIG. 16 depicts the ethanol production from Avicel by a co-culture offive S. cerevisiae strains expressing heterologous cellulases.

FIG. 17 depicts the ethanol production from Avicel by a co-culture offour S. cerevisiae strains expressing heterologous cellulases as well asthe ethanol production from strain MO288, which is expressing fourcellulases.

FIG. 18 depicts the ethanol production from Avicel by a co-culture offour S. cerevisiae strains expressing heterologous cellulases incombination with externally added cellulase.

FIG. 19 depicts the calculated enzyme savings using a co-culture of fourS. cerevisiae strains expressing heterologous cellulases or MO288 ascompared to untransformed S. cerevisiae.

FIG. 20 depicts the xylose utilization and ethanol production of M0509freezer stock, YPX-isolate and YPD-isolate.

FIG. 21 depicts the growth of M1105 (labeled “colony C2”) and M01046 inthe presence of the same medium and 8 g/L acetate at 40° C.

FIG. 22 depicts the ethanol production by M1105 (triangles) and M1088(squares) on 18% TS MS419. The experiment with M1105 had 10% lowerenzyme dose and half the inoculated cell density, but produced a higherethanol titer. The experiment with M01105 was performed at 40° C., andthe experiment with M1088 was performed at 35° C.

FIG. 23 depicts the ethanol production of M1105 where the fermentationwas only inoculated with 0.15 g/L DCW and resulted in some sugaraccumulation and 29 g/L ethanol.

FIG. 24 depicts the ethanol production of M1254 is standard IFM(circles) and low ammonium IFM (squares) conditions.

FIG. 25 depicts the specific growth rate of single colonies compared toM1254 and M1339 on complex xylose medium supplemented with a syntheticinhibitor mixture (which included 8 g/L acetate) at 40° C. The singlecolonies were screened at the same conditions as the evolution occurred.Colony C1 was renamed M1360.

FIG. 26 depicts the fermentation performance of M1360 at 40° C. onindustrially relevant fermentation medium supplemented with glucose. Thefermentation was inoculated with 60 mg/L dry cell weight of M1360.

FIG. 27 depicts the ethanol production in SSF runs on PHW (18% solids,unwashed MS149) at 35° C. and 40° C. by several strains. All reactionswere loaded with 4 mg/g “zoomerase” (Novozyme 22c).

FIG. 28 depicts cultures spotted on SC^(-URA) plates containing 0.2% ofeither CMC or lichenin or barley-β-glucan. The top two rows of eachplate were Y294 based cultures, and the bottom two rows contained M0749based strains. Numbers indicate the plasmid contained by each strain.pMU471 contains the C.f.EG and served as positive control. Plates wereincubated for 24 hours at 30° C. (pictured on the left), after whichcolonies were washed of and the plates were stained with 0.1% congo redand destained with 1% NaCl (pictured on the right).

FIG. 29 depicts SDS-PAGE analysis of the supernatants of Ce15 cellulaseproducing strains. A strain containing a plasmid with no foreign genewas used as reference strain (REF). The strain containing the plasmidpMU471 expressing C.f.EG, the most successful EG previously found wasalso included.

FIG. 30 depicts the activity of strains expressing EGs on (A) PASC (2hours) and (B) avicel (24 hours). A strain containing a plasmid with noforeign gene was used as reference strain (REF) and the strainexpressing C.f.EG (pMU471) was included as positive control.

FIG. 31 depicts the distribution of avicel conversion ability of yeastsupernatants from transformation with TrEG2 and additionalTeCBH1w/TrCBD. M1088 conversion is presented as a dark vertical line,and the dotted lines flanking this line represent the standard deviationof the measurement.

FIG. 32 depicts the conversion of Avicel in the HTP avicel assay (48hour time point) by supernatants of cellulase expressing yeast strains.M0509 is the negative control expressing no cellulases. Strain 1088 isthe parental strain expressing only CBH1, CBH2, and BGL, whereas 1179,1180, and 1181 are transformants of 1088 also expressing TrEG2.

FIG. 33 depicts ethanol production in paper sludge CBP/SSF withcellulolytic strain M1403 and non-cellulolytic background strain M1254with various amounts of commercial enzyme supplementation. Experimentalconditions: 30% solids fed batch, 10 g/l cell inoculuation, pH 5.5 andtemperature 40° C., Zoom=Novozymes 22C cellulase preparation, BGL=ABEnzymes EL2008044L BGL preparation, Xyl=AB Enzymes EL2007020L xylanasepreparation.

FIG. 34 depicts fermentation of two types of paper sludge by CBP yeast(M1179) and a control strain M0509, not expressing cellulases.Experimental conditions: 18% solids, cells loaded at 10 or 1 g/L, pH5.5, Temp: 35 C, 1 mg/g BGL and 1 mg/g Xyl loaded. BGL=AB EnzymesEL2008044L BGL preparation, Xyl=AB Enzymes EL2007020L xylanasepreparation.

FIG. 35 depicts the performance of cellulolytic yeast strain M0963 andnon-cellulolytic control strain (M0509) on 22% unwashed solids ofpretreated hardwood (PHW) (MS149) at various external cellulaseconcentrations. Experimental conditions: 22% solids fed batch, pH 5.4,temperature 35° C., all enzyme protein (EP) was “zoomerase” (Novozymes22C).

FIG. 36 depicts the performance of cellulolytic yeast strain M1284 on30% solids of washed pretreated hardwood at various initial cellloadings. Experimental conditions: 30% solids fed batch, pH 5.0,temperature 35° C., 4 mg EP=0.25 mg BGL+0.25 mg Xylanase+0.25 mgPectinase+3.25 mg Zoomerase, 20 mg EP=1 mg BGL+1 mg Xylanase+1 mgPectinase+16.7 mg Zoomerase. Zoomerase=Novozymes 22C cellulasepreparation, BGL=AB Enzymes EL2008044L BGL preparation, Xyl=AB EnzymesEL2007020L xylanase preparation, Pectinase=Genencor Multifect pectinaseFE.

FIG. 37 depicts the ethanol production in washed corn stover CBP/SSFwith cellulolytic strain M1284 and non-cellulolytic background strainM0509 with various amounts of commercial enzyme supplementation.Experimental conditions: 18% solids fed batch, 10 g/l cell inoculuation,pH 5.0 and temperature 35° C., 1 mg/g BGL and 1 mg/g xylanase loaded ineach case. BGL=AB Enzymes EL2008044L BGL preparation, Xyl=AB EnzymesEL2007020L xylanase preparation.

FIG. 38A depicts the activity on Avicel of yeast culture supernatantsexpressing different CBH1 genes. The host strain was either Y294 orM0749. The CBH1 genes are: Te, Talaromyces emersonii; Ct, Chaetomiumthermophilum; At, Acremonium thermophilum; Tr, Trichoderma reesei; Hg,Humicola grisea; Ta, Thermoascus aurantiacus. The plasmid names areindicated. Yeast were cultivated in YPD in triplicate for 3 days. Thedata are means±standard deviation.

FIG. 38B depicts the activity on Avicel of yeast culture supernatantsexpressing different CBH1 genes. The host strain is M0749. The CBH1genes are: Te, Talaromyces emersonii; Ct, Chaetomium thermophilum; At,Acremonium thermophilum; Tr, Trichoderma reesei; Hg, Humicola grisea;Ta, Thermoascus aurantiacus. The plasmid names are indicated. Yeast werecultivated in YPD in triplicate for 3 days. The data are means±standarddeviation.

FIG. 38C depicts the activity on MULac of yeast culture supernatantsexpressing different CBH1 genes. The host strain is Y294. The CBH1 genesare: Te, Talaromyces emersonii; Ct, Chaetomium thermophilum; At,Acremonium thermophilum; Tr, Trichoderma reesei; Hg, Humicola grisea;Ta, Thermoascus aurantiacus. The plasmid names are indicated. Yeast werecultivated in YPD in triplicate for 3 days. The data are means±standarddeviation.

FIG. 38D depicts the activity on MULac of yeast culture supernatantsexpressing different CBH1 genes. The host strain is M0749. The CBH1genes are: Te, Talaromyces emersonii; Ct, Chaetomium thermophilum; At,Acremonium thermophilum; Tr, Trichoderma reesei; Hg, Humicola grisea;Ta, Thermoascus aurantiacus. The plasmid names are indicated. Yeast werecultivated in YPD in triplicate for 3 days. The data are means±standarddeviation.

FIG. 38E depicts the activity on estimated CBH1 concentration (mg/L)based on MULac. The host strain is Y294. The CBH1 genes are: Te,Talaromyces emersonii; Ct, Chaetomium thermophilum; At, Acremoniumthermophilum; Tr, Trichoderma reesei; Hg, Humicola grisea; Ta,Thermoascus aurantiacus. The plasmid names are indicated. Yeast werecultivated in YPD in triplicate for 3 days. The data are means±standarddeviation.

FIG. 38F depicts the activity on estimated CBH1 concentration (mg/L)based on MULac. The host is M0749. The CBH1 genes are: Te, Talaromycesemersonii; Ct, Chaetomium thermophilum; At, Acremonium thermophilum; Tr,Trichoderma reesei; Hg, Humicola grisea; Ta, Thermoascus aurantiacus.The plasmid names are indicated. Yeast were cultivated in YPD intriplicate for 3 days. The data are means±standard deviation.

FIG. 39 shows the genes modified in yeast strain M0509.

FIG. 40 shows the yeast strains used to contruct M0509 and the relevantgenetic modifications.

FIG. 41 shows the genealogy of yeast strain M1105.

FIG. 42 shows the genealogy of yeast strain M1254.

DETAILED DESCRIPTION OF THE INVENTION

The disclosed methods and materials are useful generally in the field ofengineered yeast.

Definitions

A “vector,” e.g., a “plasmid” or “YAC” (yeast artificial chromosome)refers to an extrachromosomal element often carrying one or more genesthat are not part of the central metabolism of the cell, and is usuallyin the form of a circular double-stranded DNA molecule. Such elementsmay be autonomously replicating sequences, genome integrating sequences,phage or nucleotide sequences, linear, circular, or supercoiled, of asingle- or double-stranded DNA or RNA, derived from any source, in whicha number of nucleotide sequences have been joined or recombined into aunique construction which is capable of introducing a promoter fragmentand DNA sequence for a selected gene product along with appropriate 3′untranslated sequence into a cell. Preferably, the plasmids or vectorsof the present invention are stable and self-replicating.

An “expression vector” is a vector that is capable of directing theexpression of genes to which it is operably associated.

The term “heterologous” as used herein refers to an element of a vector,plasmid or host cell that is derived from a source other than theendogenous source. Thus, for example, a heterologous sequence could be asequence that is derived from a different gene or plasmid from the samehost, from a different strain of host cell, or from an organism of adifferent taxonomic group (e.g., different kingdom, phylum, class,order, family genus, or species, or any subgroup within one of theseclassifications). The term “heterologous” is also used synonymouslyherein with the term “exogenous.”

The term “domain” as used herein refers to a part of a molecule orstructure that shares common physical or chemical features, for examplehydrophobic, polar, globular, helical domains or properties, e.g., a DNAbinding domain or an ATP binding domain. Domains can be identified bytheir homology to conserved structural or functional motifs. Examples ofcellobiohydrolase (CBH) domains include the catalytic domain (CD) andthe cellulose binding domain (CBD).

A “nucleic acid,” “polynucleotide,” or “nucleic acid molecule” is apolymeric compound comprised of covalently linked subunits callednucleotides. Nucleic acid includes polyribonucleic acid (RNA) andpolydeoxyribonucleic acid (DNA), both of which may be single-stranded ordouble-stranded. DNA includes cDNA, genomic DNA, synthetic DNA, andsemi-synthetic DNA.

An “isolated nucleic acid molecule” or “isolated nucleic acid fragment”refers to the phosphate ester polymeric form of ribonucleosides(adenosine, guanosine, uridine or cytidine; “RNA molecules”) ordeoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, ordeoxycytidine; “DNA molecules”), or any phosphoester analogs thereof,such as phosphorothioates and thioesters, in either single strandedform, or a double-stranded helix. Double stranded DNA-DNA, DNA-RNA andRNA-RNA helices are possible. The term nucleic acid molecule, and inparticular DNA or RNA molecule, refers only to the primary and secondarystructure of the molecule, and does not limit it to any particulartertiary forms. Thus, this term includes double-stranded DNA found,inter alia, in linear or circular DNA molecules (e.g., restrictionfragments), plasmids, and chromosomes. In discussing the structure ofparticular double-stranded DNA molecules, sequences may be describedherein according to the normal convention of giving only the sequence inthe 5′ to 3′ direction along the non-transcribed strand of DNA (i.e.,the strand having a sequence homologous to the mRNA).

A “gene” refers to an assembly of nucleotides that encode a polypeptide,and includes cDNA and genomic DNA nucleic acids. “Gene” also refers to anucleic acid fragment that expresses a specific protein, includingintervening sequences (introns) between individual coding segments(exons), as well as regulatory sequences preceding (5′ non-codingsequences) and following (3′ non-coding sequences) the coding sequence.“Native gene” refers to a gene as found in nature with its ownregulatory sequences.

A nucleic acid molecule is “hybridizable” to another nucleic acidmolecule, such as a cDNA, genomic DNA, or RNA, when a single strandedform of the nucleic acid molecule can anneal to the other nucleic acidmolecule under the appropriate conditions of temperature and solutionionic strength. Hybridization and washing conditions are well known andexemplified, e.g., in Sambrook, J., Fritsch, E. F. and Maniatis, T.MOLECULAR CLONING: A LABORATORY MANUAL, Second Edition, Cold SpringHarbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter11 and Table 11.1 therein (hereinafter “Maniatis”, entirely incorporatedherein by reference). The conditions of temperature and ionic strengthdetermine the “stringency” of the hybridization. Stringency conditionscan be adjusted to screen for moderately similar fragments, such ashomologous sequences from distantly related organisms, to highly similarfragments, such as genes that duplicate functional enzymes from closelyrelated organisms. Post-hybridization washes determine stringencyconditions. One set of conditions uses a series of washes starting with6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with0.2×SSC, 0.5% SDS at 50° C. for 30 min. For more stringent conditions,washes are performed at higher temperatures in which the washes areidentical to those above except for the temperature of the final two 30min washes in 0.2×SSC, 0.5% SDS are increased to 60° C. Another set ofhighly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDSat 65° C. An additional set of highly stringent conditions are definedby hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC,0.1% SDS followed by 0.1×SSC, 0.1% SDS.

Hybridization requires that the two nucleic acids contain complementarysequences, although depending on the stringency of the hybridization,mismatches between bases are possible. The appropriate stringency forhybridizing nucleic acids depends on the length of the nucleic acids andthe degree of complementation, variables well known in the art. Thegreater the degree of similarity or homology between two nucleotidesequences, the greater the value of Tm for hybrids of nucleic acidshaving those sequences. The relative stability (corresponding to higherTm) of nucleic acid hybridizations decreases in the following order:RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotidesin length, equations for calculating Tm have been derived (see, e.g.,Maniatis at 9.50-9.51). For hybridizations with shorter nucleic acids,i.e., oligonucleotides, the position of mismatches becomes moreimportant, and the length of the oligonucleotide determines itsspecificity (see, e.g., Maniatis, at 11.7-11.8). In one embodiment thelength for a hybridizable nucleic acid is at least about 10 nucleotides.Preferably a minimum length for a hybridizable nucleic acid is at leastabout 15 nucleotides; more preferably at least about 20 nucleotides; andmost preferably the length is at least 30 nucleotides. Furthermore, theskilled artisan will recognize that the temperature and wash solutionsalt concentration may be adjusted as necessary according to factorssuch as length of the probe.

The term “percent identity”, as known in the art, is a relationshipbetween two or more polypeptide sequences or two or more polynucleotidesequences, as determined by comparing the sequences. In the art,“identity” also means the degree of sequence relatedness betweenpolypeptide or polynucleotide sequences, as the case may be, asdetermined by the match between strings of such sequences.

As known in the art, “similarity” between two polypeptides is determinedby comparing the amino acid sequence and conserved amino acidsubstitutes thereto of the polypeptide to the sequence of a secondpolypeptide.

“Identity” and “similarity” can be readily calculated by known methods,including but not limited to those described in: Computational MolecularBiology (Lesk, A. M., ed.) Oxford University Press, NY (1988);Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.)Academic Press, NY (1993); Computer Analysis of Sequence Data, Part I(Griffin, A. M., and Griffin, H. G., eds.) Humana Press, NJ (1994);Sequence Analysis in Molecular Biology (von Heinje, G., ed.) AcademicPress (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux,J., eds.) Stockton Press, NY (1991). Preferred methods to determineidentity are designed to give the best match between the sequencestested. Methods to determine identity and similarity are codified inpublicly available computer programs. Sequence alignments and percentidentity calculations may be performed using the Megalign program of theLASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.).Multiple alignments of the sequences disclosed herein were performedusing the Clustal method of alignment (Higgins and Sharp (1989) CABIOS.5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTHPENALTY=10). Default parameters for pairwise alignments using theClustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALSSAVED=5.

Suitable nucleic acid sequences or fragments thereof (isolatedpolynucleotides of the present invention) encode polypeptides that areat least about 70% to 75% identical to the amino acid sequences reportedherein, at least about 80%, 85%, or 90% identical to the amino acidsequences reported herein, or at least about 95%, 96%, 97%, 98%, 99%, or100% identical to the amino acid sequences reported herein. Suitablenucleic acid fragments are at least about 70%, 75%, or 80% identical tothe nucleic acid sequences reported herein, at least about 80%, 85%, or90% identical to the nucleic acid sequences reported herein, or at leastabout 95%, 96%, 97%, 98%, 99%, or 100% identical to the nucleic acidsequences reported herein. Suitable nucleic acid fragments not only havethe above identities/similarities but typically encode a polypeptidehaving at least 50 amino acids, at least 100 amino acids, at least 150amino acids, at least 200 amino acids, or at least 250 amino acids.

A DNA or RNA “coding region” is a DNA or RNA molecule which istranscribed and/or translated into a polypeptide in a cell in vitro orin vivo when placed under the control of appropriate regulatorysequences. “Suitable regulatory regions” refer to nucleic acid regionslocated upstream (5′ non-coding sequences), within, or downstream (3′non-coding sequences) of a coding region, and which influence thetranscription, RNA processing or stability, or translation of theassociated coding region. Regulatory regions may include promoters,translation leader sequences, RNA processing site, effector binding siteand stem-loop structure. The boundaries of the coding region aredetermined by a start codon at the 5′ (amino) terminus and a translationstop codon at the 3′ (carboxyl) terminus A coding region can include,but is not limited to, prokaryotic regions, cDNA from mRNA, genomic DNAmolecules, synthetic DNA molecules, or RNA molecules. If the codingregion is intended for expression in a eukaryotic cell, apolyadenylation signal and transcription termination sequence willusually be located 3′ to the coding region.

An “isoform” is a protein that has the same function as another proteinbut which is encoded by a different gene and may have small differencesin its sequence.

A “paralogue” is a protein encoded by a gene related by duplicationwithin a genome.

An “orthologue” is gene from a different species that has evolved from acommon ancestral gene by speciation. Normally, orthologues retain thesame function in the course of evolution as the ancestral gene.

“Open reading frame” is abbreviated ORF and means a length of nucleicacid, either DNA, cDNA or RNA, that comprises a translation start signalor initiation codon, such as an ATG or AUG, and a termination codon andcan be potentially translated into a polypeptide sequence.

“Promoter” refers to a DNA fragment capable of controlling theexpression of a coding sequence or functional RNA. In general, a codingregion is located 3′ to a promoter. Promoters may be derived in theirentirety from a native gene, or be composed of different elementsderived from different promoters found in nature, or even comprisesynthetic DNA segments. It is understood by those skilled in the artthat different promoters may direct the expression of a gene indifferent tissues or cell types, or at different stages of development,or in response to different environmental or physiological conditions.Promoters which cause a gene to be expressed in most cell types at mosttimes are commonly referred to as “constitutive promoters”. It isfurther recognized that since in most cases the exact boundaries ofregulatory sequences have not been completely defined, DNA fragments ofdifferent lengths may have identical promoter activity. A promoter isgenerally bounded at its 3′ terminus by the transcription initiationsite and extends upstream (5′ direction) to include the minimum numberof bases or elements necessary to initiate transcription at levelsdetectable above background. Within the promoter will be found atranscription initiation site (conveniently defined for example, bymapping with nuclease 51), as well as protein binding domains (consensussequences) responsible for the binding of RNA polymerase.

A coding region is “under the control” of transcriptional andtranslational control elements in a cell when RNA polymerase transcribesthe coding region into mRNA, which is then trans-RNA spliced (if thecoding region contains introns) and translated into the protein encodedby the coding region.

“Transcriptional and translational control regions” are DNA regulatoryregions, such as promoters, enhancers, terminators, and the like, thatprovide for the expression of a coding region in a host cell. Ineukaryotic cells, polyadenylation signals are control regions.

The term “operably associated” refers to the association of nucleic acidsequences on a single nucleic acid fragment so that the function of oneis affected by the other. For example, a promoter is operably associatedwith a coding region when it is capable of affecting the expression ofthat coding region (i.e., that the coding region is under thetranscriptional control of the promoter). Coding regions can be operablyassociated to regulatory regions in sense or antisense orientation.

The term “expression,” as used herein, refers to the transcription andstable accumulation of sense (mRNA) or antisense RNA derived from thenucleic acid fragment of the invention. Expression may also refer totranslation of mRNA into a polypeptide.

Host Cells Expressing Heterologous Cellulases

In order to address the limitations of the previous systems, the presentinvention provides host cells expressing heterologous cellulases thatcan be effectively and efficiently utilized to produce ethanol fromcellulose. In some embodiments, the host cells can be a yeast. Accordingto the present invention the yeast host cell can be, for example, fromthe genera Saccharomyces, Kluyveromyces, Candida, Pichia,Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, and Yarrowia.Yeast species as host cells may include, for example, S. cerevisiae, S.bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, K. lactis,K. marxianus, or K. fragilis. In some embodiments, the yeast is selectedfrom the group consisting of Saccharomyces cerevisiae,Schizzosaccharomyces pombe, Candida albicans, Pichia pastoris, Pichiastipitis, Yarrowia lipolytica, Hansenula polymorpha, Phaffia rhodozyma,Candida utilis, Arxula adeninivorans, Debaryomyces hansenii,Debaryomyces polymorphus, Schizosaccharomyces pombe and Schwanniomycesoccidentalis. In one particular embodiment, the yeast is Saccharomycescerevisiae. In another embodiment, the yeast is a thermotolerantSaccharomyces cerevisiae. The selection of an appropriate host is deemedto be within the scope of those skilled in the art from the teachingsherein.

In some embodiments of the present invention, the host cell is anoleaginous cell. According to the present invention, the oleaginous hostcell can be an oleaginous yeast cell. For example, the oleaginous yeasthost cell can be from the genera Blakeslea, Candida, Cryptococcus,Cunninghamella, Lipomyces, Mortierella, Mucor, Phycomyces, Pythium,Rhodosporidum, Rhodotorula, Trichosporon or Yarrowia. According to thepresent invention, the oleaginous host cell can be an oleaginousmicroalgae host cell. For example, the oleaginous microalgea host cellcan be from the genera Thraustochytrium or Schizochytrium. Biodieselcould then be produced from the triglyceride produced by the oleaginousorganisms using conventional lipid transesterification processes. Insome particular embodiments, the oleaginous host cells can be induced tosecrete synthesized lipids. Embodiments using oleaginous host cells areadvantegeous because they can produce biodiesel from lignocellulosicfeedstocks which, relative to oilseed substrates, are cheaper, can begrown more densely, show lower life cycle carbon dioxide emissions, andcan be cultivated on marginal lands.

In some embodiments of the present invention, the host cell is athermotolerant host cell. Thermotolerant host cells can be particularlyuseful in simultaneous saccharification and fermentation processes byallowing externally produced cellulases and ethanol-producing host cellsto perform optimally in similar temperature ranges.

Thermotolerant host cells of the invention can include, for example,Issatchenkia orientalis, Pichia mississippiensis, Pichia mexicana,Pichia farinosa, Clavispora opuntiae, Clavispora lusitaniae, Candidamexicana, Hansenula polymorpha and Kluyveromyces host cells. In someembodiments, the thermotolerant cell is an S. cerevisiae strain, orother yeast strain, that has been adapted to grow in high temperatures,for example, by selection for growth at high temperatures in a cytostat.

In some particular embodiments of the present invention, the host cellis a Kluyveromyces host cell. For example, the Kluyveromyces host cellcan be a K. lactis, K. marxianus, K. blattae, K. phaffii, K. yarrowii,K. aestuarii, K. dobzhanskii, K. wickerhamii K. thermotolerans, or K.waltii host cell. In one embodiment, the host cell is a K. lactis, or K.marxianus host cell. In another embodiment, the host cell is a K.marxianus host cell.

In some embodiments of the present invention the thermotolerant hostcell can grow at temperatures above about 30° C., about 31° C., about32° C., about 33° C., about 34° C., about 35° C., about 36° C., about37° C., about 38° C., about 39° C., about 40° C., about 41° C. or about42° C. In some embodiments of the present invention the thermotoleranthost cell can produce ethanol from cellulose at temperatures above about30° C., about 31° C., about 32° C., about 33° C., about 34° C., about35° C., about 36° C., about 37° C., about 38° C., about 39° C., about40° C., about 41° C., about 42° C., or about 43° C., or about 44° C., orabout 45° C., or about 50° C.

In some embodiments of the present invention, the thermotolerant hostcell can grow at temperatures from about 30° C. to 60° C., about 30° C.to 55° C., about 30° C. to 50° C., about 40° C. to 60° C., about 40° C.to 55° C. or about 40° C. to 50° C. In some embodiments of the presentinvention, the thermotolterant host cell can produce ethanol fromcellulose at temperatures from about 30° C. to 60° C., about 30° C. to55° C., about 30° C. to 50° C., about 40° C. to 60° C., about 40° C. to55° C. or about 40° C. to 50° C.

In some methods described herein, the host cell has the ability tometabolize xylose. Detailed information regarding the development of thexylose-utilizing technology can be found in the following publications:Kuyper M et al. FEMS Yeast Res. 4: 655-64 (2004), Kuyper M et al. FEMSYeast Res. 5:399-409 (2005), and Kuyper M et al. FEMS Yeast Res.5:925-34 (2005), which are herein incorporated by reference in theirentirety. For example, xylose-utilization can be accomplished in S.cerevisiae by heterologously expressing the xylose isomerase gene, XylA,e.g. from the anaerobic fungus Piromyces sp. E2, overexpressing five S.cerevisiae enzymes involved in the conversion of xylulose to glycolyticintermediates (xylulokinase, ribulose 5-phosphate isomerase, ribulose5-phosphate epimerase, transketolase and transaldolase) and deleting theGRE3 gene encoding aldose reductase to minimise xylitol production.

According to the methods described herein, the host cells can containantibiotic markers or can contain no antibiotic markers.

Host cells are genetically engineered (transduced or transformed ortransfected) with the polynucleotides encoding cellulases of thisinvention which are described in more detail below. The polynucleotidesencoding cellulases can be introduced to the host cell on a vector ofthe invention, which may be, for example, a cloning vector or anexpression vector comprising a sequence encoding a heterologouscellulase. The host cells can comprise polynucleotides of the inventionas integrated copies or plasmid copies.

In certain aspects, the present invention relates to host cellscontaining the polynucleotide constructs described below. The host cellsof the present invention can express one or more heterologous cellulasepolypeptides. In some embodiments, the host cell comprises a combinationof polynucleotides that encode heterologous cellulases or fragments,variants or derivatives thereof. The host cell can, for example,comprise multiple copies of the same nucleic acid sequence, for example,to increase expression levels, or the host cell can comprise acombination of unique polynucleotides. In other embodiments, the hostcell comprises a single polynucleotide that encodes a heterologouscellulase or a fragment, variant or derivative thereof. In particular,such host cells expressing a single heterologous cellulase can be usedin co-culture with other host cells of the invention comprising apolynucleotide that encodes at least one other heterologous cellulase orfragment, variant or derivative thereof.

Introduction of a polynucleotide encoding a heterologous cellulase intoa host cell can be done by methods known in the art. Introduction ofpolynucleotides encoding heterologous cellulases into, for example yeasthost cells, can be effected by lithium acetate transformation,spheroplast transformation, or transformation by electroporation, asdescribed in Current Protocols in Molecular Biology, 13.7.1-13.7.10.Introduction of the construct in other host cells can be effected bycalcium phosphate transfection, DEAE-Dextran mediated transfection, orelectroporation. (Davis, L., et al., Basic Methods in Molecular Biology,(1986)).

The transformed host cells or cell cultures, as described above, can beexamined for endoglucanase, cellobiohydrolase and/or β glucosidaseprotein content. For the use of secreted heterologous cellulases,protein content can be determined by analyzing the host (e.g., yeast)cell supernatants. In certain embodiments, high molecular weightmaterial can be recovered from the yeast cell supernatant either byacetone precipitation or by buffering the samples with disposablede-salting cartridges. Proteins, including tethered heterologouscellulases, can also be recovered and purified from recombinant yeastcell cultures by methods including spheroplast preparation and lysis,cell disruption using glass beads, and cell disruption using liquidnitrogen for example. Additional protein purification methods includeammonium sulfate or ethanol precipitation, acid extraction, anion orcation exchange chromatography, phosphocellulose chromatography,hydrophobic interaction chromatography, affinity chromatography,hydroxylapatite chromatography, gel filtration, and lectinchromatography. Protein refolding steps can be used, as necessary, incompleting configuration of the mature protein. Finally, highperformance liquid chromatography (HPLC) can be employed for finalpurification steps.

Protein analysis methods include methods such as the traditional Lowrymethod or the protein assay method according to BioRad's manufacturer'sprotocol. Using such methods, the protein content of saccharolyticenzymes can be estimated. Additionally, to accurately measure proteinconcentration a heterologous cellulase can be expressed with a tag, forexample a His-tag or HA-tag and purified by standard methods using, forexample, antibodies against the tag, a standard nickel resinpurification technique or similar approach.

The transformed host cells or cell cultures, as described above, can befurther analyzed for hydrolysis of cellulose (e.g., by a sugar detectionassay), for a particular type of cellulase activity (e.g., by measuringthe individual endoglucanase, cellobiohydrolase or β glucosidaseactivity) or for total cellulase activity. Endoglucanase activity can bedetermined, for example, by measuring an increase of reducing ends in anendoglucanase specific CMC substrate. Cellobiohydrolase activity can bemeasured, for example, by using insoluble cellulosic substrates such asthe amorphous substrate phosphoric acid swollen cellulose (PASC) ormicrocrystalline cellulose (Avicel) and determining the extent of thesubstrate's hydrolysis. β-glucosidase activity can be measured by avariety of assays, e.g., using cellobiose.

A total cellulase activity, which includes the activity ofendoglucanase, cellobiohydrolase and β-glucosidase, can hydrolyzecrystalline cellulose synergistically. Total cellulase activity can thusbe measured using insoluble substrates including pure cellulosicsubstrates such as Whatman No. 1 filter paper, cotton linter,microcrystalline cellulose, bacterial cellulose, algal cellulose, andcellulose-containing substrates such as dyed cellulose, alpha-celluloseor pretreated lignocellulose. Specific activity of cellulases can alsobe detected by methods known to one of ordinary skill in the art, suchas by the Avicel assay (described supra) that would be normalized byprotein (cellulase) concentration measured for the sample.

One aspect of the invention is thus related to the efficient productionof cellulases to aid in the digestion of cellulose and generation ofethanol. A cellulase can be any enzyme involved in cellulase digestion,metabolism and/or hydrolysis, including an endoglucanase, exogluconase,or β-glucosidase.

In additional embodiments, the transformed host cells or cell culturesare assayed for ethanol production. Ethanol production can be measuredby techniques known to one or ordinary skill in the art e.g. by astandard HPLC refractive index method.

Heterologous Cellulases

According to the present invention the expression of heterologouscellulases in a host cell can be used advantageously to produce ethanolfrom cellulosic sources. Cellulases from a variety of sources can beheterologously expressed to successfully increase efficiency of ethanolproduction. For example, the cellulases can be from fungi, bacteria,plant, protozoan or termite sources. In some embodiments, the cellulaseis a H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C.formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, S. fibuligera, C. lucknowens, R. speratus, Thermobfida fusca,Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui,Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromycesequii, Neocallimastix patricarum, Aspergillus kawachii, Heteroderaschachtii, H. jecorina, Orpinomyces sp., Irpex lacteus, Acremoniumthermophilum, Neosartorya fischeri, Chaetomium globosum, Chaetomiumthermophilum, Aspergillus fumigatus, Aspergillus terreus, NeurosporaCrassa, or Arabidopsis thaliana cellulase.

In some embodiments of the invention, multiple cellulases from a singleorganism are co-expressed in the same host cell. In some embodiments ofthe invention, multiple cellulases from different organisms areco-expressed in the same host cell. In particular, cellulases from two,three, four, five, six, seven, eight, nine or more organisms can beco-expressed in the same host cell. Similarly, the invention canencompass co-cultures of yeast strains, wherein the yeast strainsexpress different cellulases. Co-cultures can include yeast strainsexpressing heterologous cellulases from the same organisms or fromdifferent organisms. Co-cultures can include yeast strains expressingcellulases from two, three, four, five, six, seven, eight, nine or moreorganisms.

Cellulases of the present invention include both endoglucanases orexoglucanases. The cellulases can be, for example, endoglucanases,β-glucosidases or cellobiohydrolases.

In certain embodiments of the invention, the endoglucanase(s) can be anendoglucanase I or an endoglucanase II isoform, paralogue or orthologue.In some embodiments, the endoglucanase expressed by the host cells ofthe present invention can be recombinant endo-1,4-β-glucanase. Inparticular embodiments, the endoglucanase is a T. reesei, C. lacteus, C.formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, R. speratus Aspergillus kawachii, Heterodera schachtii, H.jecorina, Orpinomycess, Irpex lacteus, C. lucknowense, C. globosum,Aspergillus terreus, Aspergillus fumigatus, Neurospora crassa orAcremonium thermophilum endoglucanase. In one particular embodiment, theendoglucanase comprises an amino acid sequence selected from SEQ ID NOs:30-39 or 52-56, as shown in Table 1 below. In certain other embodiments,the endoglucanase comprises an amino acid sequence that is at leastabout 70, about 80, about 90, about 95, about 96, about 97, about 98,about 99, or 100% identical to an amino acid sequence selected from SEQID NOs: 30-39 or 52-56.

As a practical matter, whether any polypeptide is at least 70%, 80%,85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a polypeptide ofthe present invention can be determined conventionally using knowncomputer programs. Methods for determining percent identity, asdiscussed in more detail below in relation to polynucleotide identity,are also relevant for evaluating polypeptide sequence identity.

In one particular embodiment, the endoglucanase is an endoglucanase I(“eg1”) from Trichoderma reesei. In certain embodiments, theendoglucanase comprises an amino acid sequence at least about 70, about80, about 90, about 95, about 96, about 97, about 98, about 99, or 100%identical to SEQ ID NO:39.

In another particular embodiment, the endoglucanase is an endoglucanasefrom C. formosanus. In certain embodiments, the endoglucanase comprisesan amino acid sequence at least about 70, about 80, about 90, about 95,about 96, about 97, about 98, about 99, or 100% identical to SEQ IDNO:31.

In another particular embodiment, the endoglucanase is an endoglucanasefrom H. jecorina. In certain embodiments, the endoglucanase comprises anamino acid sequence at least about 70, about 80, about 90, about 95,about 96, about 97, about 98, about 99, or 100% identical to SEQ IDNO:54.

In certain embodiments, the β-glucosidase is a β-glucosidase I or aβ-glucosidase II isoform, paralogue or orthologue. In certainembodiments of the present invention the β-glucosidase is derived fromSaccharomycopsis fibuligera. In particular embodiments, theβ-glucosidase comprises an amino acid sequence at least about 70, about80, about 90, about 95, about 96, about 97, about 98, about 99, or 100%identical to SEQ ID NO:40.

In certain embodiments of the invention, the cellobiohydrolase(s) can bea cellobiohydrolase I and/or a cellobiohydrolase II isoform, paralogueor orthologue. In one particular embodiment, the cellobiohydrolasecomprises an amino acid sequence selected from SEQ ID NOs: 21-29 or 46,as shown in Table 1 below. In particular embodiments of the presentinvention the cellobiohydrolase is a cellobiohydrolase I or II fromTrichoderma reesei. In another embodiment, the cellobiohydrolasecomprises a sequence at least about 70, about 80, about 90, about 95,about 96, about 97, about 98, about 99, or 100% identical to SEQ IDNO:27 or SEQ ID NO:28.

In other particular embodiments of the present invention thecellobiohydrolase is a cellobiohydrolase I or II from T. emersonii. Inanother embodiment, the cellobiohydrolase comprises a sequence at leastabout 70, about 80, about 90, about 95, about 96, about 97, about 98,about 99, or 100% identical to SEQ ID NO:23 or SEQ ID NO:24.

In another embodiment, the cellobiohydrolase of the invention is a C.lucknowense cellobiohydrolase. In a particular embodiment, thecellobiohydrolase is C. lucknowense cellobiohydrolase Cbh2b. In oneembodiment, the cellobiohydrolase comprises a sequence at least about70, about 80, about 90, about 95, about 96, about 97, about 98, about99, or 100% identical to SEQ ID NO:25.

In some particular embodiments of the invention, the cellulase comprisesa sequence selected from the sequences in Table 1 below. The cellulasesof the invention also include cellulases that comprise a sequence atleast about 70, about 80, about 90, about 95, about 96, about 97, about98, about 99 or 100% identical to the sequences of Table 1.

Some embodiments of the invention encompass a polypeptide comprising atleast 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500 ormore consecutive amino acids of any of SEQ ID NOs:21-40, 46 or 52-56, ordomains, fragments, variants, or derivatives thereof.

TABLE 1 Cellulases used in Examples 1-11 as described below. Donororganism/ Accession number and amino acid Gene Codon-Optimized DNAsequence used sequence Cellobiohydrolases HumicolaGAATTCATGAGAACCGCTAAGTTCGCTACCTTGGCTGCCTTGGTTGCCTCT CAA35159 grisea cbh1GCTGCTGCTCAACAAGCCTGTTCCTTGACTACTGAACGTCACCCATCTTTGMRTAKFATLAALVASAAAQQATCTTGGAACAAGTGTACTGCTGGTGGTCAATGTCAAACTGTCCAAGCCTCCCSLTTERHPSLSWNKCTAGGQCATCACTTTGGACTCTAATTGGAGATGGACCCACCAAGTCTCTGGTAGTACTQTVQASITLDSNWRWTHQVSGSAACTGTTACACCGGTAATAAGTGGGACACTTCTATTTGTACTGACGCTAATNCYTGNKWDTSICTDAKSCAQGTCTTGTGCTCAAAATTGTTGTGTTGATGGTGCTGATTACACCTCCACTTANCCVDGADYTSTYGITTNGDSLSTGGTATTACCACCAACGGTGACTCTTTGTCCTTGAAGTTCGTTACTAAAGGLKFVTKGQHSTNVGSRTYLMDGTCAACATTCCACCAACGTCGGTTCTAGAACCTACTTAATGGACGGTGAAGEDKYQTFELLGNEFTFDVDVSNIACAAGTACCAAACCTTCGAATTGTTGGGTAATGAATTTACCTTCGATGTCGGCGLNGALYFVSMDADGGLSRATGTGTCTAACATCGGTTGTGGTTTGAACGGTGCTTTATACTTCGTTTCTATYPGNKAGAKYGTGYCDAQCPR GGACGCCGACGGTGGTTTGTCTCGTTACCCAGGTAATAAGGCTGGTGCCADIKFINGEANIEGWTGSTNDPNAAGTATGGTACCGGTTACTGTGATGCTCAATGCCCAAGAGACATTAAGTTC GAGRYGTCCSEMDIWEANNMAATCAACGGTGAAGCTAACATTGAAGGTTGGACTGGTTCTACCAACGACCCTAFTPHPCTIIGQSRCEGDSCGGTAAACGCTGGCGCCGGTAGATACGGTACCTGTTGTTCCGAAATGGACATTTYSNERYAGVCDPDGCDFNSYRQGGGAAGCCAACAACATGGCTACTGCTTTTACTCCACACCCATGTACCATCGNKTFYGKGMTVDTTKKITVVTATTGGTCAATCCAGATGTGAAGGTGACTCCTGTGGCGGTACCTACTCCAAQFLKDANGDLGEIKRFYVQDGKCGAAAGATACGCTGGTGTTTGTGATCCAGACGGTTGTGACTTCAACTCCTAIIPNSESTIPGVEGNSITQDWCDRCAGACAAGGTAACAAGACTTTCTATGGTAAGGGTATGACTGTCGATACCA QKVAFGDIDDFNRKGGMKQMGCCAAGAAGATCACCGTCGTCACCCAATTCTTGAAGGACGCTAACGGTGAT KALAGPMVLVMSIWDDHASNMTTAGGTGAAATTAAAAGATTCTACGTCCAAGATGGTAAGATCATCCCAAALWLDSTFPVDAAGKPGAERGACCTCTGAATCTACCATTCCAGGTGTTGAAGGTAATTCCATCACTCAAGACTGPTTSGVPAEVEAEAPNSNVVFSNGTGTGACAGACAAAAGGTTGCCTTCGGTGATATTGACGACTTCAACAGAAIRFGPIGSTVAGLPGAGNGGNNGAGGGTGGTATGAAGCAAATGGGTAAGGCTTTGGCCGGTCCAATGGTCTTGGNPPPPTTTTSSAPATTTTASAGPGTTATGTCTATTTGGGACGATCACGCTTCCAACATGTTGTGGTTGGACTCCKAGRWQQCGGIGFTGPTQCEEPACCTTCCCAGTTGATGCTGCTGGTAAGCCAGGTGCCGAAAGAGGTGCTTG YICTKLNDWYSQCL (SEQID TCCAACTACTTCCGGTGTCCCAGCTGAAGTTGAAGCCGAAGCTCCAAATT NO: 21)CTAACGTTGTCTTCTCTAACATCAGATTCGGTCCAATCGGTTCCACAGTCGCTGGTTTGCCAGGTGCTGGTAATGGTGGTAATAACGGTGGTAACCCACCACCACCAACCACTACCACTTCTTCTGCCCCAGCTACTACCACCACCGCTTCTGCTGGTCCAAAGGCTGGTAGATGGCAACAATGTGGTGGTATTGGTTTCACCGGTCCAACCCAATGTGAAGAACCATACATCTGTACCAAGTTGAACGACTGGTACTCTCAATGTTTATAACTCGAG (SEQ ID NO: 1) ThermoascusGAATTCATGTACCAAAGAGCTCTATTGTTCTCCTTCTTCTTGGCCGCCGCT AAL83303 aurantiacusAGAGCTCATGAAGCCGGTACTGTCACCGCCGAAAACCACCCATCCTTGACMYQRALLFSFFLAAARAHEAGT cbh1TTGGCAACAATGTTCCTCTGGTGGTTCTTGTACTACTCAAAACGGGAAGGTVTAENHPSLTWQQCSSGGSCTTTGTTATTGACGCTAACTGGAGATGGGTTCACACTACCTCCGGTTACACCAAQNGKVVIDANWRWVHTTSGYTCTGTTACACTGGTAACACTTGGGATACTTCCATCTGTCCAGACGACGTTACNCYTGNTWDTSICPDDVTCAQNCTGTGCTCAAAACTGTGCTTTGGACGGTGCTGACTACTCCGGTACTTACGGCALDGADYSGTYGVTTSGNALRTGTCACTACCTCTGGCAACGCGTTGAGATTGAACTTCGTCACCCAATCTTCLNFVTQSSGKNIGSRLYLLQDDTTGGTAAGAACATCGGTTCTAGATTGTACTTGTTGCAAGACGATACTACTTATYQIFKLLGQEFTFDVDVSNLPCCCAAATCTTCAAGTTGTTGGGTCAAGAGTTCACTTTCGACGTTGATGTTTCGLNGALYFVAMDADGNLSKYPCAACTTGCCTTGTGGTTTGAACGGTGCTTTGTACTTCGTTGCTATGGACGCGNKAGAKYGTGYCDSQCPRDL CGACGGTAACTTATCCAAGTACCCAGGTAACAAGGCCGGTGCCAAGTACGKFINGQANVEGWQPSANDPNAGGTACCGGTTACTGTGATTCTCAATGTCCAAGAGACCTAAAATTCATTAACGVGNHGSSCAEMDVWEANSISTAGTCAAGCTAACGTCGAAGGTTGGCAACCATCTGCTAACGATCCAAACGCCVTPHPCDTPGQTMCQGDDCGGTGGTGTCGGTAATCACGGTTCCTCCTGTGCTGAAATGGACGTTTGGGAAGCYSSTRYAGTCDTDGCDFNPYQPTAACTCTATCTCCACCGCCGTCACTCCACATCCATGTGATACCCCAGGTCAGNHSFYGPGKIVDTSSKFTVVTQAACCATGTGTCAAGGTGATGATTGTGGTGGTACCTACTCTTCCACTAGATAFITDDGTPSGTLTEIKRFYVQNGCGCTGGTACCTGTGACACCGACGGTTGTGATTTCAACCCATACCAACCAGKVIPQSESTISGVTGNSITTEYCTGTAACCACTCTTTCTACGGTCCAGGTAAGATTGTCGATACTTCTTCTAAGTAQKAAFDNTGFFTHGGLQKISQTCACTGTTGTCACTCAATTCATTACCGACGATGGTACCCCATCTGGTACCC ALAQGMVLVMSLWDDHAANMTAACTGAAATTAAGAGATTCTACGTCCAAAACGGTAAAGTCATTCCACAALWLDSTYPTDADPDTPGVARGTTCCGAAAGCACCATTTCCGGTGTTACCGGTAACTCCATCACCACTGAATACCPTTSGVPADVESQNPNSYVIYSTGTACCGCTCAAAAGGCCGCCTTTGACAACACCGGTTTCTTCACCCATGGT NIKVGPINSTFTAN (SEQID GGTTTGCAAAAGATTTCTCAAGCCTTGGCTCAAGGTATGGTTTTGGTCATG NO: 22)TCCTTGTGGGATGACCACGCTGCTAACATGTTGTGGTTGGATTCTACTTACCCAACTGACGCTGATCCAGACACCCCAGGTGTTGCTAGAGGTACTTGTCCAACCACTTCTGGTGTTCCAGCTGACGTCGAATCTCAAAACCCTAACTCTTACGTTATCTACTCTAACATCAAGGTGGGTCCAATTAACTCCACCTTCACTGC TAACTAACTCGAG (SEQID NO: 2) TalaromycesGAATTCATGCTAAGAAGAGCTTTACTATTGAGCTCTTCTGCTATCTTGGCC AAL89553 emersoniiGTTAAGGCTCAACAAGCCGGTACCGCTACTGCTGAAAACCACCCTCCATTMLRRALLLSSSAILAVKAQQAG cbh1GACCTGGCAAGAATGTACCGCTCCAGGTTCTTGTACCACCCAAAACGGTGTATAENHPPLTWQECTAPGSCTTCTGTCGTCTTGGACGCTAACTGGAGATGGGTCCACGACGTCAACGGTTAC QNGAVVLDANWRWVHDVNGYACTAACTGTTACACCGGTAACACCTGGGACCCAACTTACTGTCCAGACGATNCYTGNTWDPTYCPDDETCAQCGAAACTTGCGCTCAAAACTGTGCCTTGGACGGTGCTGACTACGAAGGTANCALDGADYEGTYGVTSSGSSLCTTACGGTGTTACCTCCTCTGGTTCTTCCTTGAAGTTGAACTTCGTCACTGGKLNFVTGSNVGSRLYLLQDDSTTTCTAACGTCGGTTCCAGATTGTATTTGTTGCAAGATGACTCCACTTACCAYQIFKLLNREFSFDVDVSNLPCGAATCTTCAAGTTGTTGAACAGAGAATTTTCTTTCGACGTCGATGTGTCCAALNGALYFVAMDADGGVSKYPNCTTGCCTTGTGGTTTGAACGGTGCTCTATACTTCGTTGCTATGGACGCTGANKAGAKYGTGYCDSQCPRDLKFTGGTGGTGTTTCCAAGTACCCAAACAACAAGGCTGGTGCCAAATACGGTAIDGEANVEGWQPSSNNANTGIGCTGGTTACTGTGACTCTCAATGTCCACGTGACTTGAAGTTTATTGATGGTGDHGSCCAEMDVWEANSISNAVTAAGCTAATGTCGAAGGTTGGCAACCATCTTCTAACAACGCTAACACTGGCPHPCDTPGQTMCSGDDCGGTYSATCGGTGACCACGGTTCTTGCTGTGCCGAAATGGACGTTTGGGAAGCCAA NDRYAGTCDPDGCDFNPYRMGCTCCATTTCCAACGCCGTCACTCCACACCCATGTGACACTCCAGGTCAAAC NTSFYGPGKIIDTTKPTATGTGTTCCGGCGATGACTGTGGTGGTACTTACTCTAACGATAGATACGCFTVVTQFLTDDGTDTGTLSEIKRTGGTACCTGTGATCCAGACGGTTGCGACTTCAATCCATACAGAATGGGTAFYIQNSNVIPQPNSDISGVTGNSIACACTTCCTTTTACGGTCCAGGCAAGATCATCGACACTACTAAGCCATTCATTEFCTAQKQAFGDTDDFSQHGCTGTTGTCACCCAATTCTTGACCGACGATGGTACTGATACCGGTACTTTGT GLAKMGAAMQQGMVLVMSLWCCGAAATCAAGAGATTCTACATCCAAAACTCTAACGTCATCCCACAACCA DDYAAQMLWLDSDYPTDADPTAATTCCGACATCTCTGGTGTCACTGGTAACTCCATTACCACCGAATTTTGTTPGIARGTCPTDSGVPSDVESQSPACCGCCCAAAAGCAAGCTTTCGGTGACACCGACGACTTCTCTCAACACGG NSYVTYSNIKFGPINSTFTASTGGTTTGGCTAAGATGGGTGCTGCTATGCAACAAGGTATGGTTTTGGTCAT (SEQ ID NO: 23)GTCTTTGTGGGACGACTACGCTGCTCAAATGTTGTGGTTGGACTCCGATTACCCAACCGATGCCGACCCAACCACCCCTGGTATCGCTAGAGGTACCTGTCCAACTGACTCTGGTGTTCCATCTGACGTCGAATCCCAATCTCCAAACTCCTACGTCACTTACTCCAACATTAAATTCGGTCCAATCAACTCCACTTTCACTG CTTCTTAACTCGAG (SEQID NO: 3) TalaromycesGAATTCATGCGTAACTTGTTGGCCTTGGCTCCAGCCGCTTTGTTGGTTGGT AAL78165 emersoniiGCTGCCGAAGCTCAACAATCCTTGTGGGGTCAATGCGGTGGTTCCTCCTGMRNLLALAPAALLVGAAEAQQS cbh2GACTGGTGCAACTTCCTGTGCCGCTGGTGCCACCTGTTCCACCATTAACCCLWGQCGGSSWTGATSCAAGATATACTACGCTCAATGTGTTCCAGCCACTGCCACTCCAACTACCTTGACTACCSTINPYYAQCVPATATPTTLTTCACCACTAAGCCAACCTCCACCGGTGGTGCTGCTCCAACCACTCCACCACTTKPTSTGGAAPTTPPPTTTGTTTCAACTACTACCGGTACTACCACCTCTCCAGTCGTCACCAGACCTGCCTCCGSPVVTRPASASGNPFEGYQLYANCCTCCGGTAATCCATTCGAAGGTTATCAATTGTACGCTAACCCTTACTACGPYYASEVISLAIPSLSSELVPKASCTTCTGAAGTCATTTCCTTGGCTATCCCATCTTTGAGCTCCGAGTTGGTCCCEVAKVPSFVWLDQAAKVPSMGAAAGGCCTCCGAAGTTGCTAAGGTCCCTTCATTTGTCTGGTTAGATCAAGCDYLKDIQSQNAAGADPPIAGIFVTGCCAAGGTTCCATCTATGGGTGATTACTTGAAGGATATTCAATCTCAAAAVYDLPDRDCAAAASNGEFSIANCGCTGCTGGTGCTGATCCACCAATCGCCGGTATTTTCGTTGTTTACGATTTNGVALYKQYIDSIREQLTTYSDVGCCAGATAGAGACTGTGCCGCCGCTGCTTCTAACGGTGAATTTTCTATCGCHTILVIEPDSLANVVTNLNVPKCCAACAACGGTGTCGCTTTATACAAACAATATATCGATTCCATTAGAGAACANAQDAYLECINYAITQLDLPNVAATTAACCACTTACTCCGACGTCCATACCATCTTGGTTATCGAACCAGACT AMYLDAGHAGWLGWQANLAPCTTTGGCTAACGTTGTCACTAACTTGAACGTTCCAAAATGTGCTAACGCTCAAQLFASVYKNASSPASVRGLAAAGATGCTTACTTGGAATGTATCAACTACGCTATTACCCAATTGGACTTGCTNVANYNAWSISRCPSYTQGDACAAACGTTGCTATGTACTTGGACGCTGGTCACGCCGGTTGGTTGGGTTGGCNCDEEDYVNALGPLFQEQGFPAAAGCCAACTTGGCCCCAGCTGCTCAATTATTCGCTTCTGTTTACAAGAACGYFIIDTSRNGVRPTKQSQWGDWCCTCTTCCCCAGCCTCTGTTAGAGGTTTGGCTACCAACGTGGCTAACTACACNVIGTGFGVRPTTDTGNPLEDAACGCCTGGTCCATTTCTAGATGTCCATCCTACACTCAAGGTGACGCTAACTFVWVKPGGESDGTSNTTSPRYDGTGATGAAGAAGATTACGTTAACGCTTTGGGTCCATTGTTCCAAGAACAAYHCGLSDALQPAPEAGTWFQAYGGTTTCCCAGCTTACTTCATCATCGACACTTCCCGTAACGGTGTCAGACCA FEQLLTNANPLF (SEQ IDNO: 24) ACTAAGCAATCTCAATGGGGTGACTGGTGTAACGTTATTGGTACCGGTTTCGGTGTTAGACCAACCACCGACACTGGTAACCCATTGGAAGACGCTTTCGTTTGGGTCAAGCCAGGTGGTGAATCCGACGGTACCTCCAACACTACTAGCCCACGTTACGATTACCACTGTGGTTTGTCTGACGCTTTGCAACCAGCTCCAGAAGCTGGTACCTGGTTCCAAGCCTACTTCGAACAATTGTTGACTAACGCC AACCCATTGTTCTAACTCGAG(SEQ ID NO: 4) Chryso-ATGGCCAAGAAGTTGTTCATTACCGCTGCCTTAGCTGCCGCAGTGCTTGCTMAKKLFITAALAAAVLAAPVIEE sporiumGCACCAGTGATCGAAGAGAGACAAAATTGCGGAGCCGTCTGGACACAGT RQNCGAVWTQCGGNGWQGPTClucknowense GCGGAGGCAACGGCTGGCAAGGCCCAACATGTTGTGCTTCTGGCTCAACGCASGSTCVAQNEWYSQCLPNSQ CBH2bTGCGTGGCACAGAACGAGTGGTATTCCCAGTGCCTTCCAAACTCCCAGGTVTSSTTPSSTSTSQRSTSTSSSTTRGACTTCTTCAACAACCCCCAGCTCAACGTCTACTTCACAGAGATCCACAASGSSSSSSTTPPPVSSPVTSIPGGAGTACCTCTTCTAGCACAACCAGAAGTGGCTCATCCTCATCTAGCAGTACGTSTASYSGNPFSGVRLFANDYYRACCCCTCCACCCGTATCAAGTCCTGTCACGAGTATCCCTGGCGGAGCAACSEVHNLAIPSMTGTLAAKASAVCTCAACAGCCAGTTATTCCGGCAATCCTTTCTCTGGAGTGAGATTATTTGCAEVPSFQWLDRNVTIDTLMVQTAAACGACTATTATAGATCAGAGGTTCACAACCTTGCAATTCCTTCTATGACLSQVRALNKAGANPPYAAQLVVGGGAACCCTAGCCGCAAAGGCTTCCGCCGTAGCAGAAGTCCCTAGTTTCCYDLPDRDCAAAASNGEFSIANGAATGGCTTGACAGAAACGTTACAATAGATACACTTATGGTACAGACTTTAGAANYRSYIDAIRKHIIEYSDIRIITCTCAGGTTAGAGCTTTGAATAAGGCCGGTGCCAACCCACCTTATGCTGCCLVIEPDSMANMVTNMNVAKCSCAATTAGTAGTCTATGACTTGCCAGATAGAGACTGTGCTGCCGCAGCTTCTNAASTYHELTVYALKQLNLPNVAATGGTGAATTTTCCATCGCAAATGGCGGAGCTGCAAACTATAGATCATA AMYLDAGHAGWLGWPANIQPACATTGATGCAATAAGAAAACACATCATTGAGTATTCTGATATTAGAATAAAELFAGIYNDAGKPAAVRGLATTCCTTGTGATTGAACCAGACTCCATGGCTAATATGGTTACCAACATGAATGNVANYNAWSIASAPSYTSPNPNTAGCCAAGTGTTCTAACGCAGCTTCCACATACCATGAGCTAACCGTATATYDEKHYIEAFSPLLNSAGFPARFIGCATTAAAACAACTGAATCTACCTAACGTTGCTATGTACTTAGATGCCGGT VDTGRNGKQPTGQQQWGDWCCATGCCGGATGGTTGGGCTGGCCTGCAAATATCCAACCCGCAGCTGAATTNVKGTGFGVRPTANTGHELVDAGTTCGCTGGAATCTACAACGACGCCGGAAAGCCCGCTGCCGTTAGAGGCTFVWVKPGGESDGTSDTSAARYDTAGCCACAAATGTTGCAAATTACAACGCTTGGTCAATTGCTAGTGCCCCTTYHCGLSDALQPAPEAGQWFQAYCTTATACCTCACCAAATCCTAACTACGATGAGAAACATTACATAGAAGCA FEQLLTNANPPF (SEQ IDNO: 25) TTTTCCCCATTGTTAAACTCCGCTGGATTCCCTGCCAGATTCATCGTGGATACCGGTAGAAACGGCAAACAACCAACTGGACAACAACAATGGGGAGATTGGTGTAACGTCAAGGGAACCGGCTTCGGCGTCAGGCCTACGGCAAACACCGGACACGAGCTAGTCGACGCTTTTGTATGGGTTAAGCCAGGTGGCGAAAGTGACGGAACAAGTGACACGAGTGCTGCAAGATACGATTACCACTGTGGTCTGTCCGACGCTTTACAGCCCGCCCCCGAGGCTGGACAATGGTTCCAGGCTTATTTTGAACAATTGTTAACGAACGCAAATCCACCATTCTAA (SEQ ID NO: 5) TalaromycesATGCTAAGAAGAGCTTTACTATTGAGCTCTTCTGCTATCTTGGCCGTTAAGMLRRALLLSSSAILAVKAQQAG emersoniiGCTCAACAAGCCGGTACCGCTACTGCTGAAAACCACCCTCCATTGACCTGTATAENHPPLTWQECTAPGSCTT cbh1 withGCAAGAATGTACCGCTCCAGGTTCTTGTACCACCCAAAACGGTGCTGTCG QNGAVVLDANWRWVHDVNGYCBD TCTTGGACGCTAACTGGAGATGGGTCCACGACGTCAACGGTTACACTAACTNCYTGNTWDPTYCPDDETCAQTGTTACACCGGTAACACCTGGGACCCAACTTACTGTCCAGACGACGAAACNCALDGADYEGTYGVTSSGSSLTTGCGCTCAAAACTGTGCCTTGGACGGTGCTGACTACGAAGGTACTTACGKLNFVTGSNVGSRLYLLQDDSTGTGTTACCTCCTCTGGTTCTTCCTTGAAGTTGAACTTCGTCACTGGTTCTAAYQIFKLLNREFSFDVDVSNLPCGCGTCGGTTCCAGATTGTATTTGTTGCAAGATGACTCCACTTACCAAATCTTLNGALYFVAMDADGGVSKYPNCAAGTTGTTGAACAGAGAATTTTCTTTCGACGTCGATGTGTCCAACTTGCCNKAGAKYGTGYCDSQCPRDLKFTTGTGGTTTGAACGGTGCTCTATACTTCGTTGCTATGGACGCTGATGGTGGIDGEANVEGWQPSSNNANTGIGTGTTTCCAAGTACCCAAACAACAAGGCTGGTGCCAAATACGGTACTGGTTDHGSCCAEMDVWEANSISNAVTACTGTGACTCTCAATGTCCACGTGACTTGAAGTTTATTGATGGTGAAGCTAPHPCDTPGQTMCSGDDCGGTYSATGTCGAAGGTTGGCAACCATCTTCTAACAACGCTAACACTGGCATCGGT NDRYAGTCDPDGCDFNPYRMGGACCACGGTTCTTGCTGTGCCGAAATGGACGTTTGGGAAGCCAACTCCATNTSFYGPGKIIDTTKPFTVVTQFLTTCCAACGCCGTCACTCCACACCCATGTGACACTCCAGGTCAAACTATGTGTDDGTDTGTLSEIKRFYIQNSNVITTCCGGCGATGACTGTGGTGGTACTTACTCTAACGATAGATACGCTGGTACPQPNSDISGVTGNSITTEFCTAQKCTGTGATCCAGACGGTTGCGACTTCAATCCATACAGAATGGGTAACACTT QAFGDTDDFSQHGGLAKMGAACCTTTTACGGTCCAGGCAAGATCATCGACACTACTAAGCCATTCACTGTTG MQQGMVLVMSLWDDYAAQMLTCACCCAATTCTTGACCGACGATGGTACTGATACCGGTACTTTGTCCGAAAWLDSDYPTDADPTTPGIARGTCPTCAAGAGATTCTACATCCAAAACTCTAACGTCATCCCACAACCAAATTCCTDSGVPSDVESQSPNSYVTYSNIGACATCTCTGGTGTCACTGGTAACTCCATTACCACCGAATTTTGTACCGCCKFGPINSTFTASNPPGGNRGTTTTCAAAAGCAAGCTTTCGGTGACACCGACGACTTCTCTCAACACGGTGGTTTRRPATTTGSSPGPTQSHYGQCGGGGCTAAGATGGGTGCTGCTATGCAACAAGGTATGGTTTTGGTCATGTCTTTIGYSGPTVCASGTTCQVLNPYYSGTGGGACGACTACGCTGCTCAAATGTTGTGGTTGGACTCCGATTACCCAA QCL (SEQ ID NO: 26)CCGATGCCGACCCAACCACCCCTGGTATCGCTAGAGGTACCTGTCCAACTGACTCTGGTGTTCCATCTGACGTCGAATCCCAATCTCCAAACTCCTACGTCACTTACTCCAACATTAAATTCGGTCCAATCAACTCCACTTTCACTGCTTCTAACCCTCCAGGTGGTAACAGAGGTACTACCACTACTCGTAGGCCAGCTACTACAACTGGTTCTTCCCCAGGCCCAACCCAATCCCACTACGGTCAATGTGGTGGTATCGGTTACTCTGGTCCAACCGTCTGTGCTTCTGGTACTACCTGTCAAGTTTTAAACCCATACTACTCTCAATGTTTGTAG (SEQ ID NO: 6) TrichodermaATGGTCTCCTTCACCTCCCTGCTGGCCGGCGTTGCCGCTATCTCTGGTGTC ACCESSION NO.:CAA49596 reesei CBH1 CTAGCAGCCCCTGCCGCAGAAGTTGAACCTGTCGCAGTTGAGAAACGTGAMVSFTSLLAGVAAISGVLAAPAGGCCGAAGCAGAAGCTCAATCCGCTTGTACCCTACAATCCGAAACTCACCAEVEPVAVEKREAEAEAQSACTCACCATTGACCTGGCAAAAGTGTTCTAGCGGTGGAACTTGTACTCAACAALQSETHPPLTWQKCSSGGTCTQACTGGTTCTGTTGTTATCGACGCTAACTGGAGATGGACACACGCCACTAAQTGSVVIDANWRWTHATNSSTNCTCTTCTACCAACTGTTACGACGGTAACACTTGGTCTTCCACTTTATGTCCCYDGNTWSSTLCPDNETCAKNCAGATAACGAAACTTGTGCTAAGAATTGCTGTTTGGACGGTGCCGCCTACGCLDGAAYASTYGVTTSGNSLSIGCTTCTACCTACGGTGTTACCACCTCCGGTAACTCCTTGTCTATTGGTTTCGTFVTQSAQKNVGARLYLMASDTTCACTCAATCCGCTCAAAAGAACGTTGGTGCTAGATTGTACTTGATGGCTTCYQEFTLLGNEFSFDVDVSQLPCGTGACACTACTTATCAAGAATTTACTTTGTTGGGTAACGAATTTTCTTTCGALNGALYFVSMDADGGVSKYPTNTGTTGACGTTTCCCAATTGCCATGTGGCTTGAACGGTGCTTTGTACTTTGTTAGAKYGTGYCDSQCPRDLKFICTCTATGGATGCTGACGGTGGTGTTTCTAAGTACCCAACTAACACTGCCGGNGQANVEGWEPSSNNANTGIGGTGCTAAGTACGGTACTGGTTACTGTGATTCTCAATGTCCACGTGACTTGAAHGSCCSEMDIWEANSISEALTPHGTTCATTAACGGTCAAGCCAACGTCGAAGGTTGGGAACCATCCTCCAACAPCTTVGQEICEGDGCGGTYSDNACGCTAACACCGGTATCGGTGGTCACGGTTCCTGTTGTTCCGAAATGGACRYGGTCDPDGCDWNPYRLGNTSATCTGGGAAGCTAACAGTATTTCTGAAGCTTTGACACCACACCCATGCACFYGPGSSFTLDTTKKLTVVTQFECACTGTCGGTCAAGAAATTTGTGAAGGTGATGGATGTGGTGGAACCTACTTSGAINRYYVQNGVTFQQPNAECTGATAACAGATACGGTGGTACTTGTGACCCAGACGGTTGTGACTGGAACLGSYSGNELNDDYCTAEEAEFGCCATACAGATTGGGTAACACTTCTTTCTATGGTCCAGGTTCTTCTTTCACCTGSSFSDKGGLTQFKKATSGGMVTGGATACCACCAAGAAGTTGACTGTTGTTACCCAATTCGAAACTTCTGGTGLVMSLWDDYYANMLWLDSTYP CTATCAACAGATACTACGTTCAAAACGGTGTCACCTTCCAACAACCAAACTNETSSTPGAVRGSCSTSSGVPAGCTGAATTGGGTTCTTACTCTGGTAATGAATTGAACGACGACTACTGTACCQVESQSPNAKVTFSNIKFGPIGSTGCTGAAGAAGCTGAATTTGGTGGTTCCTCTTTCTCCGACAAGGGTGGTTTGGNPSGGNPPGGNRGTTTTRRPATACCCAATTCAAGAAGGCTACCTCCGGTGGTATGGTTTTGGTTATGTCCTTGTTGSSPGPTQSHYGQCGGIGYSGTGGGATGATTACTACGCAAACATGTTATGGTTAGACAGTACTTACCCAAC PTVCASGTTCQVLNPYYSQCLTAACGAAACCTCCTCTACTCCAGGTGCTGTCAGAGGTTCCTGTTCTACCTC (SEQ ID NO: 27)TTCTGGTGTTCCAGCTCAAGTTGAATCTCAATCTCCAAACGCTAAGGTCAC [SECRETION SIGNAL:1-33 TTTCTCCAACATCAAGTTCGGTCCAATCGGTTCCACTGGTAATCCATCTGG CATALYTICDOMAIN: 41-465 TGGAAACCCTCCAGGTGGTAACAGAGGTACTACCACTACTCGTAGGCCAGCELLULOSE-BINDING DOMAIN:CTACTACAACTGGTTCTTCCCCAGGCCCAACCCAATCCCACTACGGTCAAT 503-535]GTGGTGGTATCGGTTACTCTGGTCCAACCGTCTGTGCTTCTGGTACTACCTGTCAAGTTTTAAACCCATACTACTCTCAATGTTTGTAA (SEQ ID NO: 7) TrichodermaATGGTCTCCTTCACCTCCCTGCTGGCCGGCGTTGCCGCTATCTCTGGTGTC ACCESSION NO.:reesei CBH2 CTAGCAGCCCCTGCCGCAGAAGTTGAACCTGTCGCAGTTGAGAAACGTGAAAA72922AAA34210 GGCCGAAGCAGAAGCTGTCCCATTAGAAGAAAGACAAGCCTGCTCCTCTGMIVGILTTLATLATLAASVPLEETTTGGGGTCAATGTGGTGGTCAAAACTGGTCTGGTCCAACTTGTTGTGCTTRQACSSVWGQCGGQNWSGPTCCCGGTTCTACCTGTGTTTACTCCAACGACTACTATTCCCAATGTTTGCCAGCASGSTCVYSNDYYSQCLPGAAGTGCTGCTTCCTCTTCCTCTTCAACTAGAGCTGCTTCTACAACTTCTAGGGTSSSSSTRAASTTSRVSPTTSRSSSCTCCCCAACCACTTCCAGATCCTCTTCTGCTACTCCACCACCAGGTTCTACATPPPGSTTTRVPPVGSGTATYSTACCACTAGAGTTCCACCAGTCGGTTCCGGTACTGCTACTTACTCTGGTAAGNPFVGVTPWANAYYASEVSSLCCCTTTCGTCGGTGTTACTCCATGGGCTAACGCTTACTACGCTTCTGAAGTAIPSLTGAMATAAAAVAKVPSFTTCTTCTTTGGCTATCCCATCTTTGACTGGTGCTATGGCTACCGCTGCTGCTMWLDTLDKTPLMEQTLADIRTAGCTGTCGCCAAAGTTCCATCCTTCATGTGGTTGGACACCTTGGACAAAACTNKNGGNYAGQFVVYDLPDRDC CCATTAATGGAACAAACCTTGGCAGACATAAGGACTGCTAACAAGAACGAALASNGEYSIADGGVAKYKNYGCGGTAACTACGCTGGTCAATTTGTTGTGTACGACTTGCCAGACAGAGACIDTIRQIVVEYSDIRTLLVIEPDSLTGTGCTGCTTTGGCTTCCAACGGTGAATACTCCATCGCTGACGGTGGTGTCANLVTNLGTPKCANAQSAYLECGCCAAGTACAAGAACTACATTGATACCATTAGACAAATCGTTGTCGAATAINYAVTQLNLPNVAMYLDAGHACTCTGACATCAGAACCTTGTTAGTCATCGAACCAGATTCTTTAGCCAATTTGWLGWPANQDPAAQLFANVYKAGTCACCAACTTGGGTACTCCAAAGTGTGCTAACGCTCAATCTGCCTACTTNASSPRALRGLATNVANYNGWAGAATGTATCAATTATGCAGTTACCCAATTGAACTTGCCAAACGTTGCTATNITSPPSYTQGNAVYNEKLYIHAIGTACTTGGACGCTGGTCACGCCGGTTGGTTGGGTTGGCCAGCTAACCAAGGRLLANHGWSNAFFITDQGRSGACCCAGCCGCTCAATTATTCGCCAACGTTTACAAGAATGCCTCTTCTCCTAKQPTGQQQWGDWCNVIGTGFGIGAGCCTTGCGTGGTTTGGCTACTAACGTCGCTAACTACAACGGTTGGAACRPSANTGDSLLDSFVWVKPGGEATCACTTCTCCACCATCTTACACCCAAGGTAACGCTGTTTACAACGAAAACDGTSDSSAPRFDSHCALPDALQGTTGTACATTCACGCTATCGGTCCATTATTGGCTAACCATGGTTGGTCTAAPAAQAGAWFQAYFVQLLTNAN CGCCTTCTTCATCACCGACCAAGGTAGATCCGGTAAACAACCAACTGGTCPSFL (SEQ ID NO: 28) AACAACAATGGGGTGATTGGTGTAACGTCATCGGTACTGGTTTCGGTATCAGACCATCCGCTAACACTGGTGATTCCTTGTTGGATTCCTTCGTCTGGGTTAAGCCAGGTGGTGAATGTGATGGCACCTCTGATTCCTCTGCTCCAAGATTCGATTCCCACTGCGCCTTGCCAGACGCTTTGCAACCAGCCCCACAAGCTGGTGCATGGTTCCAAGCTTACTTTGTCCAATTGTTGACCAACGCTAACCCATC TTTCTTGTAA (SEQ IDNO: 8) Chaetomium TTAATTAAACAATGATGTACAAGAAATTTGCAGCCCTAGCTGCTTTAGTTGAM711862 thermophilum CAGGAGCTTCCGCTCAACAGGCATGTTCATTGACTGCCGAAAATCATCCAMMYKKFAALAALVAGASAQQA CBH1TCCTTAACGTGGAAGAGATGCACGTCAGGAGGTTCATGCTCCACTGTAAACSLTAENHPSLTWKRCTSGGSCSCGGAGCTGTCACAATAGATGCAAATTGGAGATGGACCCACACTGTGTCCG TVNGAVTIDANWRWTHGTAGTACAAACTGCTACACCGGTAATCAATGGGATACGTCTTTGTGTACATVSGSTNCYTGNQWDTSLCTDGGATGGAAAGTCATGCGCTCAGACCTGTTGCGTGGATGGAGCAGACTACTCKSCAQTCCVDGADYSSTYGITTSTTCTACTTACGGAATCACGACATCAGGTGACAGTCTTAATTTGAAATTCGT GDSLNLKFVTKHQYGAACCAAGCACCAGTACGGAACAAATGTAGGCTCCAGAGTGTACTTAATGGTNVGSRVYLMENDTKYQMFELLAGAACGATACCAAATATCAAATGTTCGAGTTATTAGGCAATGAGTTTACCGNEFTFDVDVSNLGCGLNGALYTTTGACGTAGACGTTAGCAATTTGGGTTGCGGATTAAACGGCGCCCTTTAC FVSMDADGGMSKYSGNTTCGTGTCTATGGATGCTGACGGAGGTATGTCAAAGTATTCTGGTAACAAKAGAKYGTGYCDAQCPRDLKFIAGCCGGAGCAAAGTACGGTACAGGTTATTGTGACGCTCAGTGCCCTAGAG NGEANVGNWTPSTNDANAGFGATTTGAAGTTTATCAACGGAGAAGCCAACGTTGGTAACTGGACGCCAAGT RYGSCCSEMDVWEANNMACTAACGACGCAAACGCTGGATTCGGCAGATACGGTAGTTGTTGCTCAGAATAFTPHPCTTVGQSRCEADTCGAATGGACGTGTGGGAGGCCAATAACATGGCAACCGCTTTTACTCCTCACCGTYSSDRYAGVCDPDGCDFNAYCATGTACAACTGTTGGACAATCTAGATGTGAAGCCGACACGTGCGGTGGC RQGDKTFYGKGMTVDACCTACAGTAGCGATAGGTATGCAGGAGTATGTGATCCTGACGGTTGCGATNKKMTVVTQFHKNSAGVLSEITTTCAATGCTTATAGACAAGGAGACAAAACGTTTTATGGTAAAGGTATGAKRFYVQDGKIIANAESKIPGNPGCCGTCGATACTAACAAGAAGATGACTGTGGTTACCCAGTTCCACAAGAAC NSITQEYCDAQKVAFTCAGCTGGAGTATTGTCTGAAATTAAAAGATTCTACGTCCAGGATGGAAA SNTDDFNRKGGMAQMSKALAGGATTATTGCTAATGCCGAGAGTAAGATACCAGGTAACCCTGGAAATAGTA PMVLVMSVWDDHYANMLWLDTCACACAGGAATACTGTGACGCTCAGAAGGTAGCTTTTAGCAACACCGAT STYPIDQAGAPGAERGACPGACTTCAATAGAAAGGGTGGAATGGCTCAAATGAGTAAGGCTTTAGCCGGTTSGVPAEIEAQVPNSNVIFSNIRTCCAATGGTGTTGGTGATGTCTGTTTGGGATGATCACTATGCAAACATGCTFGPIGSTVPGLDGSNPGNPTTTVTTGGCTTGACAGCACCTATCCTATCGACCAAGCCGGAGCCCCAGGTGCTG VPPASTSTSRPTSAAAGGGGTGCATGTCCAACCACGAGTGGTGTGCCCGCCGAGATTGAAGCTSTSSPVSTPTGQPGGCTTQKWGQCAAGTGCCTAATAGTAACGTTATCTTTTCCAATATAAGATTCGGACCAATCCGGIGYTGCTNCVAGTTCTQLNGGATCCACTGTTCCAGGTTTGGATGGATCTAATCCTGGCAACCCAACAAC PWYSQCL (SEQ ID NO:29) CACGGTAGTCCCTCCAGCTTCAACTTCCACAAGTAGACCAACAAGTTCAACGTCCAGTCCAGTGTCTACTCCTACCGGACAACCAGGAGGCTGTACCACTCAGAAATGGGGTCAATGCGGTGGAATTGGCTATACAGGTTGTACGAATTGCGTTGCAGGAACCACTTGTACACAGTTAAACCCTTGGTACTCACAATGCCT ATAAGGCGCGCC (SEQ IDNO: 9) Acremonium ATGTATACCAAATTTGCTGCATTGGCCGCTTTAGTTGCAACAGTAAGAGGTMYTKFAALAALVATVRGQAAC thermophilumCAAGCCGCTTGTTCTCTAACCGCAGAAACTCACCCATCTCTACAATGGCASLTAETHPSLQWQKCTAPGSCTT CBH1GAAATGCACAGCCCCTGGATCTTGTACAACTGTCTCCGGCCAAGTCACCAVSGQVTIDANWRWLHQTNSSTNTTGACGCTAATTGGAGATGGCTTCACCAAACTAACTCTTCAACGAATTGTTCYTGNEWDTSICSSDTDCATKCATACCGGTAACGAATGGGATACTTCCATATGTTCATCCGATACAGACTGCCLDGADYTGTYGVTASGNSLNLGCAACGAAATGTTGTTTAGATGGAGCAGACTATACGGGAACTTATGGTGTKFVTQGPYSKNIGSRMYLMESESTACAGCCTCAGGTAATTCCCTAAACCTTAAGTTCGTAACTCAAGGACCATKYQGFTLLGQEFTFDVDVSNLGATAGTAAGAATATCGGCTCTAGAATGTACTTGATGGAAAGTGAGAGCAAACGLNGALYFVSMDLDGGVSKYTTATCAGGGTTTTACGTTATTGGGACAAGAGTTTACATTTGATGTTGATGTGTNKAGAKYGTGYCDSQCPRDLKAGTAACTTAGGTTGCGGCCTAAACGGCGCCTTGTACTTCGTTTCTATGGATFINGQANIDGWQPSSNDANAGLCTTGATGGAGGTGTATCAAAATACACGACCAACAAGGCTGGAGCCAAATAGNHGSCCSEMDIWEANKVSAAYTGGTACGGGATATTGTGACAGCCAATGCCCTAGAGACTTAAAGTTCATTATPHPCTTIGQTMCTGDDCGGTYSACGGTCAGGCAAATATTGACGGCTGGCAACCAAGCAGTAACGACGCTAATSDRYAGICDPDGCDFNSYRMGDGCCGGACTAGGTAACCATGGCTCATGTTGTTCCGAAATGGATATCTGGGATSFYGPGKTVDTGSKFTVVTQFLAGCCAATAAGGTGTCCGCTGCCTACACCCCCCATCCATGCACGACAATCGTGSDGNLSEIKRFYVQNGKVIPNGTCAGACAATGTGTACCGGTGATGACTGTGGAGGCACATACTCAAGTGATSESKIAGVSGNSITTDFCTAQKTAGGTACGCCGGTATATGTGATCCTGACGGTTGCGATTTCAACTCTTATAGAAFGDTNVFEERGGLAQMGKAL ATGGGAGATACATCCTTTTACGGCCCCGGTAAAACAGTTGATACGGGTAGAEPMVLVLSVWDDHAVNMLWLTAAGTTCACTGTTGTTACTCAGTTCTTAACAGGTTCAGACGGCAATCTTAGDSTYPTDSTKPGAARGDCPITSGTGAAATCAAAAGATTCTACGTTCAGAATGGAAAAGTCATTCCTAATTCCGVPADVESQAPNSNVIYSNIRFGPIAGAGTAAGATTGCTGGTGTGTCTGGTAACAGTATCACGACCGACTTCTGTNSTYTGTPSGGNPPGGGTTTTTTACCGCCCAAAAGACTGCCTTTGGAGATACGAATGTTTTCGAGGAAAGGGGTTTSKPSGPTTTTNPSGPQQTHWCGGTCTTGCTCAAATGGGCAAGGCTTTGGCCGAACCAATGGTATTAGTCC GQCGGQGWTGPTVCQSPYTCKTATCCGTTTGGGATGATCATGCAGTGAATATGCTTTGGCTTGATAGCACCT YSNDWYSQCL (SEQ IDNO: 46) ACCCTACTGACAGCACCAAGCCAGGAGCTGCCAGAGGTGACTGTCCTATCACAAGTGGCGTTCCAGCAGATGTAGAGAGCCAAGCTCCAAACTCCAATGTGATCTATTCTAACATCAGATTTGGCCCCATTAATAGTACCTATACAGGAACGCCCTCTGGTGGTAACCCTCCAGGCGGAGGCACCACAACTACCACGACCACAACGACTTCAAAGCCTTCTGGCCCTACGACAACTACCAATCCTTCCGGACCACAGCAAACTCACTGGGGTCAGTGTGGAGGCCAAGGATGGACGGGTCCTACCGTGTGTCAATCACCTTACACATGCAAATACAGTAATGACTGGTACT CTCAGTGTTTATAA (SEQID NO: 45) Endoglucanases CoptotermesATGAGATTTCCTTCCATATTCACCGCTGTTTTGTTCGCAGCCTCAAGTGCTTMRFPSIFTAVLFAASSALAECTK lacteus EGTAGCAGAATGTACTAAGGGTGGATGTACTAACAAGAATGGATACATAGTTGGCTNKNGYIVHDKHVGDIQNRCATGATAAGCACGTCGGTGACATCCAGAATAGAGACACTTTGGACCCTCCDTLDPPDLDYEKDVGVTVSGGTAGACTTAGATTATGAAAAGGACGTGGGAGTAACCGTGTCCGGTGGAACCCLSQRLVSTWNGKKVVGSRLYIVTTAGTCAAAGATTAGTCTCAACTTGGAACGGTAAGAAAGTCGTGGGAAGTDEADEKYQLFTFVGKEFTYTVDAGATTGTATATTGTGGACGAAGCCGACGAGAAATATCAATTATTCACATTTMSQIQCGINAALYTVEMPAAGKGTCGGTAAGGAGTTCACCTATACCGTTGATATGTCCCAGATCCAATGTGGATPGGVKYGYGYCDANCVDGDC ATCAATGCCGCATTATACACAGTGGAAATGCCTGCCGCTGGAAAGACCCCCMEFDIQEASNKAIVYTTHSCQSTGGAGGTGTTAAGTATGGATATGGATATTGTGATGCCAACTGCGTGGATGQTSGCDTSGCGYNPYRDSGDKAGAGATTGTTGTATGGAGTTCGATATCCAAGAAGCTTCTAACAAGGCAATCFWGTTINVNQPVTIVTQFIGSGSSGTTTACACCACCCATTCCTGTCAAAGTCAAACTTCAGGTTGCGATACCTCALTEVKRLCVQGGKTFPPAKSLTGGATGCGGTTACAACCCTTACAGAGACAGTGGTGACAAGGCATTCTGGGG DSYCNANDYRSLRTMGASMARAACAACTATAAACGTAAACCAGCCTGTGACAATTGTAACACAGTTTATCG GHVVVFSLWDSNGMSWMDGGGTTCTGGTAGTTCCTTAACTGAAGTCAAAAGATTGTGCGTGCAAGGTGGANAGPCTSYNIESLESSQPNLKVTAAGACCTTCCCTCCAGCCAAATCATTAACCGACAGTTATTGTAATGCCAAC WSNVKYGEIDSPY (SEQID GACTATAGAAGTTTGAGAACTATGGGTGCATCCATGGCTAGAGGACACGT NO: 30)TGTTGTGTTTTCTTTGTGGGATTCTAATGGTATGAGTTGGATGGATGGAGGTAACGCCGGTCCTTGTACCTCATATAATATTGAATCTTTGGAATCCAGTCAGCCAAACTTAAAGGTCACATGGTCAAACGTGAAATACGGAGAGATCGATT CTCCTTATTAA (SEQ IDNO: 10) Coptotermes ATGAGATTCCCTTCCATTTTCACTGCTGTTTTGTTCGCAGCCTCAAGTGCTTBAB40697 formosanus TAGCAGCCTATGACTACAAGACAGTATTGAAGAACTCCTTGTTGTTCTACGMRFPSIFTAVLFAASSALAAYDY EGAAGCTCAAAGAAGTGGAAAATTGCCTGCAGACCAGAAGGTGACCTGGAG KTVLKNSLLFYEAQRSGKLPADAAAAGATTCCGCATTAAACGACAAGGGACAGAAGGGAGAGGACTTAACT QKVTWRKDSALNDKGQKGEDLGGAGGTTATTACGACGCCGGAGACTTTGTGAAGTTCGGTTTTCCAATGGCATGGYYDAGDFVKFGFPMAYTVTACACAGTTACCGTGTTGGCCTGGGGTTTAGTCGATTATGAATCTGCTTACTVLAWGLVDYESAYSTAGALD AGTACTGCGGGTGCCTTGGATGATGGTAGAAAGGCCTTGAAATGGGGTACDGRKALKWGTDYFLKAHTAANAGATTATTTCTTGAAAGCACATACCGCTGCCAATGAGTTTTACGGACAGGTEFYGQVGQGDVDHAYWGRPED GGGTCAGGGAGATGTGGATCATGCTTACTGGGGACGTCCTGAGGACATGAMTMSRPAYKIDTSKPGSDLAAECTATGTCTAGACCAGCTTACAAGATCGATACATCAAAACCTGGTAGTGACTTAAALAATAIAYKSADSTYSNNTAGCTGCAGAAACAGCAGCCGCTTTAGCAGCAACCGCAATAGCTTACAAGLITHAKQLFDFANNYRGKYSDSITCAGCCGATTCTACCTACAGTAACAACTTAATTACTCATGCAAAGCAGTTGTDAKNFYASGDYKDELVWAAATTCGATTTTGCAAACAATTATAGAGGAAAGTACTCTGATAGTATTACCGATWLYRATNDNTYLTKAESLYNEFGCCAAGAATTTCTATGCATCCGGTGATTATAAGGACGAATTAGTATGGGCTGLGSWNGAFNWDNKISGVQVL GCAGCCTGGTTGTATAGAGCTACAAATGATAACACTTACTTAACCAAAGCLAKLTSKQAYKDKVQGYVDYLCGAATCATTGTATAATGAATTTGGTTTAGGATCTTGGAACGGTGCATTCAAVSSQKKTPKGLVYIDQWGTLRHTTGGGATAACAAGATATCCGGAGTTCAGGTCTTATTAGCCAAATTGACATCAANSALIALQAADLGINAASYRCAAACAAGCATACAAAGATAAAGTTCAGGGTTATGTTGATTACTTAGTCTCQYAKKQIDYALGDGGRSYVVG CTCTCAAAAGAAAACTCCAAAGGGATTGGTCTATATTGACCAATGGGGAAFGTNPPVRPHHRSSSCPDAPAACCCTTAAGACACGCAGCTAATAGTGCCTTGATCGCTTTACAGGCCGCTGATTDWNTYNSAGPNAHVLTGALVG TGGGTATAAACGCTGCTAGTTATAGACAATACGCAAAGAAGCAAATTGATGPDSNDSYTDSRSDYISNEVATDTATGCCTTAGGTGACGGAGGTCGTTCTTACGTGGTCGGATTCGGAACTAAC YNAGFQSAVAGLLKAGV(SEQ CCTCCAGTAAGACCTCATCATAGATCCAGTTCCTGTCCTGACGCACCAGCC ID NO: 31)GCTTGCGACTGGAATACTTACAACTCTGCCGGACCAAATGCCCACGTCTTGACCGGAGCCTTAGTAGGTGGACCAGATTCCAACGATAGTTACACAGATTCACGTTCTGATTATATCAGTAACGAAGTCGCTACTGATTACAATGCCGGTTTCCAATCTGCAGTTGCTGGTTTGTTGAAAGCCGGAGTATAA (SEQ ID NO: 11) NasutitermesATGAGATTTCCATCTATTTTCACTGCCGTCTTATTTGCAGCCTCCAGTGCATMRFPSIFTAVLFAASSALAAYDY takasa-TAGCAGCCTATGATTATAAACAAGTTTTGAGAGATTCCTTATTGTTCTACGKQVLRDSLLFYEAQRSGRLPAD goensis EGAAGCTCAGAGAAGCGGTAGATTACCAGCAGACCAGAAGGTCACTTGGAG QKVTWRKDSALNDQGDQGQDLAAAAGATTCAGCCTTGAATGATCAGGGAGATCAAGGTCAAGACTTAACCGTGGYFDAGDFVKFGFPMAYTATGAGGTTATTTTGACGCCGGTGATTTTGTGAAATTTGGTTTCCCAATGGCATVLAWGLIDFEAGYSSAGALDDGATACTGCTACCGTCTTGGCCTGGGGTTTAATCGATTTTGAGGCAGGATACARKAVKWATDYFIKAHTSQNEFYGTTCCGCTGGTGCCTTGGATGACGGTAGAAAAGCAGTAAAGTGGGCAACT GQVGQGDADHAFWGRPEDMTGATTACTTTATAAAGGCCCACACTTCACAGAATGAGTTTTACGGACAAGTCMARPAYKIDTSRPGSDLAGETAGGTCAGGGTGACGCTGATCACGCTTTCTGGGGACGTCCTGAAGATATGACAALAAASIVFRNVDGTYSNNLLCATGGCTAGACCAGCCTACAAGATTGACACCAGCAGACCAGGTAGTGACTTHARQLFDFANNYRGKYSDSITTAGCGGGTGAAACCGCAGCGGCATTGGCAGCTGCCAGTATCGTGTTTAGA DARNFYASADYRDELVWAAAWAATGTTGATGGTACATACTCTAACAACTTACTTACTCATGCCAGACAATTALYRATNDNTYLNTAESLYDEFGTTTGACTTTGCAAATAACTACAGAGGAAAATACTCAGATTCCATAACCGA LQNWGGGLNWDSKVSGVQVLLCGCTAGAAACTTTTACGCCAGTGCAGATTACCGTGACGAATTGGTTTGGGCAKLTNKQAYKDTVQSYVNYLINTGCCGCATGGTTGTACAGAGCTACAAATGACAACACTTACTTGAATACCG NQQKTPKGLLYIDMWGTLRHACAGAATCCTTGTATGATGAATTTGGATTGCAGAACTGGGGTGGAGGGTTAANAAFIMLEAAELGLSASSYRQFAACTGGGATTCAAAGGTGTCTGGTGTCCAGGTCTTGTTAGCAAAATTGACCAQTQIDYALGDGGRSFVCGFGSAACAAACAGGCTTACAAAGATACTGTGCAGTCTTACGTGAATTACCTGATTNPPTRPHHRSSSCPPAPATCDWNAATAACCAGCAAAAGACCCCAAAAGGATTGTTATACATTGATATGTGGGGTFNSPDPNYHVLSGALVGGPDQTACATTGAGACACGCCGCAAATGCTGCATTCATCATGTTGGAAGCTGCCG NDNYVDDRSDYVHNEVATDYNAGTTGGGTTTATCCGCATCATCTTACAGACAGTTTGCTCAAACTCAGATCG AGFQSALAALVALGY (SEQID ACTACGCTTTGGGTGACGGTGGAAGAAGTTTCGTCTGTGGTTTTGGTTCAA NO: 32)ACCCTCCTACAAGACCACATCATCGTTCTTCCAGTTGCCCGCCTGCCCCAGCAACTTGTGACTGGAATACATTCAACTCACCTGACCCAAATTACCACGTGTTATCTGGAGCTTTGGTAGGAGGACCAGATCAAAACGATAATTATGTGGATGATAGATCCGACTACGTCCATAACGAAGTGGCAACCGACTACAACGCCGGATTTCAGAGTGCTTTGGCAGCCTTAGTTGCTTTGGGTTATTAA (SEQ ID NO: 12) CoptotermesATGAGATTCCCTAGTATTTTCACTGCCGTCTTATTTGCAGCCAGTTCTGCTTMRFPSIFTAVLFAASSALAAYDY acinaciformisTAGCCGCATATGATTATACCACAGTTTTGAAAAGTTCCTTATTGTTCTACGTTVLKSSLLFYEAQRSGKLPADQ EGAAGCTCAAAGATCCGGTAAGTTGCCAGCCGACCAGAAGGTCACTTGGAGA KVTWRKDSALDDKGNNGEDLTAAAGATTCAGCATTAGACGATAAAGGAAATAATGGAGAGGACTTAACAG GGYYDAGDFVKFGFPLAYTATVGAGGTTATTATGACGCTGGTGATTTTGTGAAGTTTGGTTTTCCTTTAGCATALAWGLVDYEAGYSSAGATDDGCACCGCTACTGTTTTAGCCTGGGGTTTGGTGGACTATGAAGCGGGTTACTCRKAVKWATDYLLKAHTAATEL ATCCGCTGGAGCCACAGATGACGGTAGAAAGGCAGTGAAATGGGCAACCYGQVGDGDADHAYWGRPEDM GACTATTTGTTGAAGGCACATACTGCCGCTACCGAGTTATACGGACAGGTCTMARPAYKIDASRPGSDLAGETGGGGACGGTGACGCCGATCACGCATATTGGGGACGTCCTGAAGATATGACAAALAAASIVFKGVDSSYSDNLTATGGCTAGACCAGCATACAAGATCGACGCTAGCAGACCAGGATCTGACTLAHAKQLFDFADNYRGKYSDSITAGCGGGTGAAACCGCTGCCGCTTTAGCCGCTGCATCCATAGTTTTCAAAGTQASNFYASGDYKDELVWAATGTGTAGATTCTTCATATTCTGACAACTTGTTAGCTCACGCTAAACAGTTATWLYRATNDNTYLTKAESLYNEFTTGATTTCGCTGACAATTATAGAGGAAAATACAGTGATTCCATAACACAA GLGNWNGAFNWDNKVSGVQVGCTTCAAACTTTTACGCCTCCGGAGATTACAAAGACGAGTTAGTCTGGGCTLLAKLTSKQAYKDTVQGYVDY GCCACTTGGTTGTACAGAGCAACCAACGATAATACATATTTGACCAAAGCLINNQQKTPKGLLYIDQWGTLRAGAATCCTTGTACAACGAGTTCGGATTAGGAAACTGGAACGGAGCCTTTAHAANAALIILQAADLGISADSYRATTGGGACAACAAGGTGTCCGGTGTTCAGGTGTTGTTAGCCAAATTGACCTQFAKKQIDYALGDGGRSYVVGFCCAAGCAGGCTTATAAAGACACCGTTCAAGGATACGTCGATTATTTGATTAGDNPPTHPHHRSSSCPDAPAVCACAATCAGCAAAAGACCCCAAAGGGTTTGTTATACATAGACCAATGGGGGDWNTFNSPDPNFHVLTGALVGGACCTTGAGACACGCAGCTAATGCTGCCTTAATAATCTTACAGGCTGCTGATPDQNDNYVDDRSDYVSNEVAT TTGGGTATTTCTGCCGACAGTTATAGACAATTCGCAAAGAAGCAAATAGADYNAGFQSAVAALVTLGV (SEQTTACGCTTTAGGTGACGGAGGTAGATCATATGTAGTTGGTTTTGGAGACAA ID NO: 33)TCCTCCAACACATCCTCATCACCGTTCTTCCTCATGCCCTGACGCCCCAGCAGTATGCGATTGGAATACTTTCAATTCACCTGATCCAAACTTTCATGTCTTAACCGGAGCTTTAGTGGGAGGTCCTGATCAGAACGATAACTACGTTGATGATCGTTCTGACTACGTGTCCAACGAGGTTGCAACCGACTATAATGCAGGATTCCAAAGTGCTGTGGCCGCTTTAGTTACTTTAGGAGTTTAA (SEQ ID NO: 13) MastotermesATGAGATTCCCAAGTATATTTACTGCTGTTTTGTTCGCAGCCAGTTCTGCTTMRFPSIFTAVLFAASSALAAYDY darwinensisTAGCAGCCTATGATTACAATGACGTATTAACCAAAAGTTTGTTGTTCTACGNDVLTKSLLFYEAQRSGKLPSD EGAAGCTCAAAGATCCGGTAAGTTACCTTCTGATCAGAAAGTCACCTGGAGA QKVTWRKDSALNDKGQNGEDLAAAGATTCAGCATTAAACGATAAGGGACAAAATGGTGAGGACTTAACTGG TGGYYDAGDYVKFGFPMAYTATGGATATTATGACGCCGGTGATTACGTGAAGTTTGGTTTTCCAATGGCATATVLAWGLVDHPAGYSSAGVLDTACTGCTACCGTTTTGGCTTGGGGTTTAGTGGACCATCCTGCCGGATACAGDGRKAVKWVTDYLIKAHVSKN TTCTGCGGGTGTCTTGGATGATGGTAGAAAAGCTGTGAAGTGGGTTACCGELYGQVGDGDADHAYWGRPED ATTACTTAATCAAAGCCCACGTATCAAAGAACGAATTATACGGACAGGTCMTMARPAYKIDTSRPGSDLAGEGGTGACGGTGACGCAGATCACGCTTATTGGGGACGTCCAGAGGATATGACTAAALAAASIVFKSTDSNYANTAATGGCAAGACCAGCATACAAAATAGACACTTCAAGACCAGGTTCCGACTLLTHAKQLFDFANNYRGKYSDSTAGCGGGTGAAACCGCAGCGGCATTGGCTGCTGCATCTATTGTGTTTAAGTITQASNFYSSSDYKDELVWAAVCAACAGATTCTAATTACGCCAACACCTTATTGACCCACGCAAAACAATTATWLYRATNDQTYLTTAEKLYSDLTCGACTTTGCCAATAACTATAGAGGTAAGTATAGTGATTCCATAACACAGGLQSWNGGFTWDTKISGVEVLLGCATCTAATTTCTACAGTAGTTCCGACTATAAAGATGAATTGGTTTGGGCAAKITGKQAYKDKVKGYCDYISGGCTGTATGGTTGTACAGAGCCACTAACGATCAGACCTATTTGACAACTGCASQQKTPKGLVYIDKWGSLRMA GAGAAGTTATACTCAGACTTGGGATTACAGTCCTGGAACGGAGGTTTCACANAAYICAVAADVGISSTAYRQATGGGACACCAAAATTAGTGGAGTAGAAGTGTTATTGGCTAAGATTACTGFAKTQINYILGDAGRSFVVGYGGTAAACAGGCATATAAGGACAAAGTAAAGGGATATTGTGATTATATCTCANNPPTHPHHRSSSCPDAPATCDGGATCTCAGCAGAAAACACCTAAAGGATTAGTTTACATAGATAAGTGGGG WNNYNSANPNPHVLYGALVGGTTCCTTAAGAATGGCCGCAAACGCCGCATATATTTGCGCTGTAGCCGCAGAPDSNDNYQDLRSDYVANEVAT CGTCGGAATCAGTTCAACAGCTTACAGACAGTTCGCCAAAACACAGATTADYNAAFQSLLALIVDLGL (SEQATTACATATTGGGTGATGCCGGACGTTCTTTTGTGGTTGGTTACGGAAACA ID NO: 34)ACCCACCTACACACCCACATCACAGATCCAGTTCATGTCCTGACGCCCCAGCAACATGCGATTGGAATAACTACAACAGTGCTAACCCTAATCCACATGTTTTATACGGTGCATTAGTTGGTGGACCAGATTCCAACGATAATTATCAAGACTTAAGATCAGATTATGTCGCCAACGAAGTGGCAACAGACTACAATGCAGCCTTCCAGTCATTGTTAGCATTAATCGTGGACTTAGGTTTGTAA (SEQ ID NO: 14) NasutitermesATGAGATTTCCATCTATTTTCACTGCCGTCTTATTTGCAGCCTCAAGTGCTTMRFPSIFTAVLFAASSALAAYDY walkeri EGTAGCAGCCTATGATTACAAACAAGTATTGAGAGATTCCTTATTGTTCTACGKQVLRDSLLFYEAQRSGRLPAD AAGCTCAGAGAAGCGGTAGATTACCAGCAGACCAGAAGGTCACCTGGAGQKVTWRKDSALNDQGEQGQDL AAAAGATTCCGCCTTGAATGATCAGGGAGAGCAAGGTCAAGACTTAACCGTGGYFDAGDFVKFGFPMAYTATGAGGTTATTTTGACGCCGGTGATTTTGTGAAGTTTGGATTCCCAATGGCTTVLAWGLIDFEAGYSSAGALDDGATACAGCAACCGTTTTGGCCTGGGGTTTAATCGACTTTGAAGCCGGTTACTRKAVKWATDYFIKAHTSQNEFYCTTCTGCTGGTGCCTTGGACGATGGTAGAAAAGCAGTAAAGTGGGCTACT GQVGQGDVDHAYWGRPEDMTGATTACTTTATAAAAGCCCATACTTCTCAAAACGAGTTTTACGGACAAGTCMARPAYKIDTSRPGSDLAGETAGGTCAGGGTGACGTAGATCACGCATATTGGGGACGTCCTGAAGATATGACAALAAASIVFKNVDGTYSNNLLAATGGCTAGACCAGCCTACAAGATTGATACCAGCAGACCAGGTAGTGACTTHARQLFDFANNYRGKYSDSITTAGCAGGAGAAACTGCTGCAGCTTTGGCTGCCGCATCCATCGTTTTCAAGADARNFYASADYRDELVWAAAWATGTAGATGGTACATATTCCAACAACTTACTTACTCATGCTAGACAGTTGTLYRATNDNSYLNTAESLYNEFGTTGATTTCGCCAACAATTACAGAGGAAAATACTCTGATAGTATTACCGATGLQNWGGGLNWDSKVSGVQVLL CAAGAAACTTTTACGCTAGTGCCGACTATAGAGATGAGTTAGTCTGGGCAAKLTNKQEYKDTIQSYVNYLINGCTGCCTGGTTGTACAGAGCAACCAACGACAATTCTTACTTGAACACTGCTNQQKTPKGLLYIDMWGTLRHA GAATCATTATACAACGAGTTTGGATTGCAAAATTGGGGTGGAGGGTTAAAANAAFIMLEAADLGLSASSYRQCTGGGATTCTAAAGTGAGTGGTGTTCAAGTTTTGTTAGCCAAGTTGACCAAFAQTQIDYALGDGGRSFVCGFGCAAACAAGAGTATAAGGACACTATTCAATCATACGTGAATTACTTAATCASNPPTRPHHRSSSCPPAPATCDWATAACCAACAGAAAACTCCAAAGGGATTGTTATACATTGACATGTGGGGGNTFNSPDPNYNVLSGALVGGPDACCTTGAGACACGCAGCTAACGCAGCCTTTATAATGTTAGAAGCTGCCGA QNDNYVDDRSDYVHNEVATDYCTTAGGTTTATCCGCTTCATCTTATAGACAGTTCGCCCAAACACAAATAGA NAGFQSALAALVALGY(SEQ ID CTACGCATTGGGGGACGGTGGACGTTCTTTTGTCTGTGGTTTCGGTTCTAA NO: 35)TCCTCCAACTAGACCTCATCATAGATCCAGTTCATGCCCGCCTGCTCCAGCTACCTGTGATTGGAATACATTCAATTCTCCTGACCCAAACTACAATGTTTTATCCGGTGCCTTGGTTGGTGGTCCTGACCAGAATGATAACTACGTGGACGATAGAAGTGATTATGTCCATAATGAGGTAGCAACTGACTACAATGCCGGTTTCCAATCAGCCTTAGCCGCTTTAGTCGCCTTAGGTTACTAA (SEQ ID NO: 15)Reticulitermes ATGAGATTCCCAAGTATATTTACTGCCGTCTTATTTGCAGCCTCCAGTGCAAB019095 speratus EG TTAGCCGCTTATGACTACAAAACAGTATTGTCCAATTCCTTGTTGTTCTACMRFPSIFTAVLFAASSALAAYDYGAAGCTCAAAGATCCGGTAAGTTACCTTCTGACCAGAAAGTGACCTGGAGKTVLSNSLLFYEAQRSGKLPSDQAAAGGATTCAGCATTAAACGACAAAGGACAAAAGGGTGAGGACTTAACC KVTWRKDSALNDKGQKGEDLTGGTGGATATTACGACGCCGGAGACTTTGTGAAATTTGGTTTTCCAATGGCTGGYYDAGDFVKFGFPMAYTVTTACACAGTTACCGTATTGGCATGGGGTGTTATTGATTACGAATCCGCCTACVLAWGVIDYESAYSAAGALDSGTCTGCCGCAGGAGCTTTAGATTCAGGTAGAAAGGCCTTGAAATATGGGACRKALKYGTDYFLKAHTAANEFYCGACTATTTCTTAAAGGCACATACAGCAGCTAACGAGTTTTACGGACAGG GQVGQGDVDHAYWGRPEDMTTGGGTCAAGGTGACGTTGACCACGCATACTGGGGACGTCCTGAAGATATGMSRPAYKIDTSKPGSDLAAETAACCATGAGCAGACCAGCATACAAAATAGACACTTCTAAGCCTGGTTCCGAAALAATAIAYKSADATYSNNLITCTTAGCTGCAGAGACTGCAGCTGCATTAGCAGCCACAGCTATTGCATACAHAKQLFDFANNYRGKYSDSITDAATCTGCCGATGCAACATATTCCAACAATTTGATAACACATGCAAAACAA AKNFYASGDYKDELVWAAAWLTTATTCGACTTTGCCAACAATTACAGAGGAAAATATTCCGATAGTATTACCYRATNDNTYLTKAESLYNEFGLGATGCCAAGAACTTTTATGCTTCTGGTGATTACAAAGACGAATTGGTATGGGNFNGAFNWDNKVSGVQVLLA GCCGCTGCATGGTTGTACAGAGCAACCAATGACAACACATATTTGACTAAKLTSKQVYKDKVQSYVDYLISSGGCAGAATCCTTATACAATGAATTTGGTTTGGGAAACTTCAATGGTGCCTTQKKTPKGLVYIDQWGTLRHAA CAATTGGGATAACAAAGTCTCCGGAGTCCAGGTGTTATTGGCCAAGTTAANSALIALQAADLGINAATYRAYCCTCAAAACAAGTGTATAAGGATAAGGTACAGTCTTACGTGGACTATTTGAKKQIDYALGDGGRSYVIGFGTATCTCCTCACAAAAAAAGACACCAAAAGGTTTAGTGTACATCGATCAATGNPPVRPHHRSSSCPDAPAVCDWGGGTACTTTAAGACACGCAGCTAATTCTGCTTTGATCGCTTTGCAGGCAGCNTYNSAGPNAHVLTGALVGGPDTGACTTAGGAATTAACGCTGCTACTTACAGAGCCTACGCAAAGAAGCAAASNDSYTDARSDYISNEVATDYNTCGACTATGCTTTGGGTGATGGTGGAAGATCCTATGTTATTGGATTTGGGA AGFQSAVAGLLKAGV (SEQID CCAACCCTCCAGTAAGACCACATCACAGAAGTTCATCTTGCCCAGATGCA NO: 36)CCAGCTGTCTGCGATTGGAACACCTATAACTCCGCTGGTCCAAACGCCCACGTGTTAACCGGTGCATTGGTTGGAGGACCTGATAGTAATGATAGTTATACCGATGCTCGTTCTGACTACATATCCAACGAAGTGGCAACTGATTACAATGCGGGTTTCCAATCCGCTGTCGCTGGATTATTGAAGGCGGGTGTCTAA (SEQ ID NO: 16)Neosartorya ATGAGATTTCCATCTATTTTCACTGCAGTTTTGTTCGCAGCCAGTTCCGCTTXM_001258277 fischeri EGTGGCCCAACAGATCGGGTCCATCGCCGAAAATCATCCTGAGTTGACAACCMRFPSIFTAVLFAASSALAQQIGTATAGATGCTCCTCTCAAGCTGGATGCGTAGCACAGAGTACTTCCGTCGTGSIAENHPELTTYRCSSQAGCVAQTTAGATATTAACGCTCATTGGATTCATCAAAACGGTGCCCAAACAAGTTGCSTSVVLDINAHWIHQNGAQTSCACTACCTCAAGTGGATTGGACCCTTCATTGTGCCCTGATAAAGTCACCTGTTTSSGLDPSLCPDKVTCSQNCVVTCTCAGAACTGCGTAGTCGAAGGAATAACCGACTACTCATCTTTTGGTGTGEGITDYSSFGVQNSGDAMTLRQCAAAACTCCGGAGATGCAATGACATTAAGACAGTATCAAGTTCAAAATGGYQVQNGQIKTLRPRVYLLAEDGACAGATCAAAACATTGCGTCCTAGAGTGTACTTGTTAGCTGAGGATGGAAINYSKLQLLNQEFTFDVDASKLPTCAATTACTCCAAATTGCAGTTGTTGAACCAAGAGTTTACTTTCGATGTGGCGMNGALYLSEMDASGGRSALACGCTTCCAAATTGCCTTGTGGTATGAATGGAGCTTTATATTTGTCAGAAANPAGATYGTGYCDAQCFNPGPTGGATGCTTCTGGTGGACGTTCTGCCTTGAACCCAGCGGGTGCCACATATGWINGEANTAGAGACCQEMDLW GAACAGGTTACTGTGATGCCCAGTGCTTCAACCCAGGTCCATGGATAAATEANSRSTIFSPHPCTTAGLYACTGGAGAAGCAAATACTGCTGGAGCCGGTGCATGTTGCCAAGAGATGGACTTGAECYSICDGYGCTYNPYELGAATGGGAAGCCAACTCCCGTTCTACCATTTTCAGTCCTCACCCATGTACAACKDYYGYGLTIDTAKPITVVTQFTGCGGGTTTGTATGCCTGTACTGGAGCTGAGTGCTACTCAATCTGTGACGGMTADNTATGTLAEIRRLYVQDGTTATGGTTGCACTTACAACCCTTATGAATTAGGAGCCAAAGATTACTATGGKVIGNTAVAMTEAFCSSSRTFEETTACGGTTTGACTATTGACACCGCAAAGCCAATAACAGTGGTTACTCAGTTLGGLQRMGEALGRGMVPVFSI TATGACCGCTGATAATACAGCAACCGGTACATTAGCAGAGATCAGAAGATWDDPGLWMHWLDSDGAGPCG TATATGTTCAAGATGGTAAAGTAATCGGAAATACAGCCGTGGCCATGACCNTEGDPAFIQANYPNTAVTFSKVGAGGCATTTTGTAGTTCTAGTAGAACATTTGAAGAGTTAGGTGGTTTGCAA RWGDIGSTYSS (SEQ IDNO: 37) AGAATGGGAGAAGCTTTAGGTAGAGGAATGGTGCCAGTTTTCTCAATATGGGACGATCCTGGTTTGTGGATGCATTGGTTAGATTCTGACGGTGCAGGACCTTGTGGTAATACTGAAGGTGATCCTGCCTTCATTCAGGCTAACTACCCAAATACCGCCGTAACATTCTCCAAGGTGAGATGGGGAGATATCGGTTCTACCTA TAGTTCTTAA (SEQ IDNO: 17) ReticulitermesATGAGATTTCCATCTATTTTCACTGCTGTTTTGTTCGCAGCCTCAAGTGCTT DQ014512 flavipesEG TAGCACAATGGATGCAGATCGGTGGTAAGCAGAAATATCCTGCCTTTAAGMRFPSIFTAVLFAASSALAQWMCCAGGTGCTAAGTACGGAAGAGGTTATTGTGACGGACAGTGCCCTCACGAQIGGKQKYPAFKPGAKYGRGYC CATGAAGGTGTCTAGTGGAAGAGCAAACGTTGACGGATGGAAGCCACAADGQCPHDMKVSSGRANVDGWK GACAACGACGAAAATAGTGGAAATGGAAAATTGGGTACATGTTGCTGGGAPQDNDENSGNGKLGTCCWEMD GATGGATATATGGGAAGGAAACTTAGTGTCCCAAGCCTACACCGTTCACGIWEGNLVSQAYTVHAGSKSGQYCTGGTTCCAAGTCCGGACAATATGAGTGTACTGGAACACAATGCGGTGACECTGTQCGDTDSGERFKGTCDKACCGACAGTGGTGAAAGATTCAAGGGAACATGCGATAAAGATGGTTGTGA DGCDFASYRWGATDYYGPGKTTTTCGCAAGTTACAGATGGGGAGCTACAGACTATTACGGTCCTGGAAAGAVDTKQPMTVVTQFIGDPLTEIKRCCGTGGACACCAAACAGCCAATGACAGTCGTGACCCAGTTCATTGGTGACVYVQGGKVINNSKTSNLGSVYDCCTTTGACTGAGATAAAGAGAGTTTATGTACAAGGAGGAAAAGTCATAAASLTEAFCDDTKQVTGDTNDFKACAATTCCAAAACATCTAACTTAGGTTCAGTGTACGATTCTTTGACTGAGGCKGGMSGFSKNLDTPQVLVMSL CTTCTGCGATGACACCAAACAGGTTACAGGTGATACAAATGACTTTAAGGWDDHTANMLWLDSTYPTDSTKCTAAAGGAGGTATGTCTGGATTCTCCAAGAACTTAGACACCCCACAAGTTTPGAARGTCAVTSGDPKDVESKQTGGTGATGTCTTTATGGGATGACCATACAGCTAATATGTTATGGTTAGATTANSQVVYSDIKFGPINSTYKANCTACTTATCCTACCGATAGTACAAAGCCAGGTGCCGCAAGAGGTACTTGT (SEQ ID NO: 38)GCCGTCACCTCCGGGGACCCTAAAGATGTGGAATCCAAGCAAGCCAACTCTCAGGTAGTTTACAGTGACATTAAGTTTGGTCCTATTAATTCAACATACAA AGCAAATTAA (SEQ IDNO: 18) Trichoderma ATGGTCTCCTTCACCTCCCTGCTGGCCGGCGTTGCCGCTATCTCTGGTGTCCAB003694 reesei EGI TAGCAGCCCCTGCCGCAGAAGTTGAACCTGTCGCAGTTGAGAAACGTGAGMVSFTSLLAGVAAISGVLAAPA GCCGAAGCAGAAGCTCAACAACCAGGAACATCAACACCAGAAGTCCATCAEVEPVAVEKREAEAEAQQPGTCAAAGTTAACAACCTATAAATGTACTAAGAGTGGAGGGTGTGTAGCGCAGSTPEVHPKLTTYKCTKSGGCVAGACACAAGTGTGGTCTTAGACTGGAATTATCGTTGGATGCATGATGCCAAT QDTSVVLDWNYRWMHDANYNTATAATTCCTGTACTGTTAACGGCGGTGTTAACACTACGTTATGCCCCGATSCTVNGGVNTTLCPDEATCGKNGAAGCGACTTGTGGTAAGAATTGTTTTATTGAAGGGGTTGACTACGCCGCTCFIEGVDYAASGVTTSGSSLTMNAGTGGTGTTACGACGAGTGGGTCATCCTTGACGATGAATCAATACATGCCTQYMPSSSGGYSSVSPRLYLLDSDTCTTCTAGTGGTGGGTATTCCTCTGTGTCTCCAAGGCTGTATTTATTGGATTGEYVMLKLNGQELSFDVDLSALCCGATGGGGAATATGTTATGTTAAAATTAAATGGGCAAGAACTGAGTTTT PCGENGSLYLSQMDENGGANQGATGTGGATCTATCTGCATTACCTTGTGGAGAAAATGGTAGTCTTTATTTAYNTAGANYGSGYCDAQCPVQT TCACAAATGGACGAAAACGGCGGAGCCAATCAGTACAATACAGCTGGTGCWRNGTLNTSHQGFCCNEMDILETAATTATGGTTCAGGCTATTGTGATGCTCAATGTCCAGTGCAGACTTGGAGGNSRANALTPHSCTATACDSAGGAATGGCACCTTAAACACATCACATCAAGGATTTTGCTGTAACGAAATGGCGFNPYGSGYKSYYGPGDTVDTACATATTAGAAGGTAATTCAAGAGCTAATGCACTAACTCCGCACTCTTGTASKTFTIITQFNTDNGSPSGNLVSICTGCGACCGCATGTGATTCTGCCGGTTGTGGTTTCAACCCTTATGGTTCTGTRKYQQNGVDIPSAQPGGDTISSGTTATAAGAGTTACTACGGTCCGGGAGACACCGTGGATACGTCAAAGACC CPSASAYGGLATMGKALSSGMTTCACTATAATCACTCAGTTTAACACAGATAACGGATCTCCGAGTGGTAATVLVFSIWNDNSQYMNWLDSGNTTGGTGAGTATTACTAGGAAATATCAGCAGAACGGTGTTGATATTCCGTCCAGPCSSTEGNPSNILANNPNTHVGCGCAGCCAGGCGGTGACACTATATCTAGCTGTCCTTCCGCCAGTGCCTATVFSNIRWGDIGSTTNSTAPPPPPAGGCGGACTTGCTACAATGGGTAAGGCATTGTCCTCAGGTATGGTCCTAGTASSTTFSTTRRSSTTSSSPSCTQTHTTTTCTATTTGGAATGATAATTCACAATACATGAATTGGCTGGATTCTGGTWGQCGGIGYSGCKTCTSGTTCQAATGCAGGCCCTTGCTCCTCTACAGAAGGTAACCCAAGCAATATACTAGC YSNDYYSQC (SEQ ID NO:39) TAATAACCCAAATACTCATGTTGTCTTTAGTAATATTAGATGGGGCGATATAGGTAGCACTACGAACAGTACCGCACCTCCTCCTCCACCTGCTAGCTCCACGACATTTTCCACTACTAGAAGGTCCAGCACTACCAGCTCATCACCATCTTGTACTCAAACCCATTGGGGACAGTGTGGTGGTATAGGTTACAGCGGTTGCAAAACTTGCACATCTGGTACTACATGCCAATACAGTAATGACTATTACTCAC AATGTTAA (SEQ ID NO:19) Aspergillus TTAATTAAAATGAGAATTTCTAACTTGATTGTTGCTGCTTCTGCTGCTACTAMRISNLIVAASAATMVSALPSRQ kawachiiTGGTTTCTGCTTTGCCATCTAGACAAATGAAAAAGAGGGATTCTGGTTTTAMKKRDSGFKWVGTSESGAEFGS EgAAATGGGTTGGTACTTCTGAATCTGGTGCTGAATTTGGTTCTGCTTTACCAGALPGTLGTDYTWPETSKIQVLRGTACTTTGGGTACTGATTATACTTGGCCAGAAACTTCTAAAATTCAAGTTTNKGMNIFRIPFLMERLTPDGLTGTGAGAAACAAGGGTATGAACATTTTTAGAATACCATTCTTGATGGAAAGASFASTYLSDLKSTVEFVTNSGAYTTAACTCCAGATGGTTTGACTGGTTCTTTTGCTTCTACTTACTTGTCTGATTAVLDPHNYGRFDGSIIESTSDFKTGAAGTCAACTGTTGAATTTGTTACTAATTCTGGTGCTTATGCTGTTTTAGATWWKNVATEFADNDKVIFDTNTCCACATAATTACGGTAGATTCGATGGTTCTATTATTGAATCTACTTCTGATNEYHDMEQSLVLNLNQAAINGITTTAAGACTTGGTGGAAAAATGTTGCTACTGAATTTGCTGATAACGATAAGRAAGATTQYIFVEGNAYTGAWGTTATTTTCGATACAAACAACGAATATCATGATATGGAACAATCTTTGGTTDWTTYNDDLSGLTDSEDKIIYETTGAATTTGAACCAAGCTGCTATTAATGGTATTAGAGCTGCTGGTGCTACTMHQYLDSDSSGTSETCVSSTIGKACTCAATACATTTTCGTTGAAGGTAATGCTTATACTGGTGCTTGGGATTGGERIEKATEWLKTNNKQGIIGEFAACTACTTACAATGATGATTTGTCTGGTTTAACTGATTCTGAAGATAAGATAGGVNSVCEEAVEGMLAYMSENATATACGAAATGCATCAATACTTGGATTCTGATTCTTCTGGTACATCTGAA SDVWVGASWWSAGPWWGTYMACTTGTGTTTCTTCTACTATTGGTAAAGAAAGAATTGAAAAGGCTACTGAAYSLEPTDGTAYSTYLPILEKYFPSTGGTTGAAAACTAACAACAAGCAAGGTATTATTGGTGAATTTGCAGGTGGGDASSSSSASASVAAATSAVSTTTGTTAATTCTGTTTGTGAAGAGGCTGTTGAAGGAATGTTGGCTTATATGTCTTAAFEQTTTPATQVEIASSSSSSTGAAAATTCTGATGTTTGGGTTGGTGCTTCTTGGTGGTCTGCTGGTCCATGSAVAASQTTLSKVKSKSKSPCKLGTGGGGTACTTACATGTATTCTTTGGAACCAACTGATGGTACTGCTTATTCSSATSSAVSSAAAVTTPAVAATTTACTTATTTGCCAATTTTGGAAAAATACTTCCCATCTGGTGATGCTTCATCAPAAAPTSSSVAFATTSVYVPTTTTCTTCATCTGCTTCAGCTTCAGTTGCAGCCGCTACTTCTGCTGTTTCTACTAAAAPSQVSSSAAASSSGVVGVSCTACTACAGCTGCATTTGAACAAACTACTACTCCAGCTACTCAAGTTGAAADPQGPSATNSAGEVNQYYQCGGTTGCTTCTTCTTCATCTTCATCATCAGCTGTTGCTGCTTCACAAACTACTTTINWTGPTVCASPYTCKVQNDYYGTCTAAGGTTAAGTCTAAATCTAAATCTCCATGTAAATTGTCATCTGCTAC YQCVAE (SEQ ID NO:52) TTCATCTGCTGTTTCATCAGCTGCTGCAGTTACTACACCTGCAGTTGCAGCTACAACTCCAGCTGCTGCTCCAACTTCTTCTTCTGTTGCTTTTGCTACTACTTCTGTTTACGTTCCAACTACTACTGCTGCTGCACCATCTCAAGTTTCATCTTCAGCTGCAGCTTCATCTTCAGGTGTTGTTGGTGTTTCTGATCCACAAGGTCCATCTGCTACTAATTCTGCTGGTGAAGTTAATCAATATTACCAATGTGGTGGTATTAATTGGACTGGTCCAACTGTTTGTGCTTCTCCATATACTTGTAAGGTTCAAAACGATTACTACTATCAATGTGTTGCTGAATTATAAGGCGCGCC (SEQ ID NO: 47)Heterodera TTAATTAAAATGCATTGGGCTGATGTTGCTTGTTCTAGACCACCATGGCCAMHWADVACSRPPWPRDSVKAL schachtiiAGAGATTCTGTTAAAGCTTTGAAGTGTAATTGGAACGCTAATGTTATTAGAKCNWNANVIRGAMGVDEGGYL Eng1GGTGCTATGGGTGTTGATGAAGGTGGTTATTTGTCTGATGCTAATACTGCTSDANTAYNLMVAVIEAAISNGIYTACAATTTGATGGTTGCTGTTATTGAAGCTGCTATTTCTAATGGTATCTACGVIVDWHAHNAHPDEAVKFFTRITTATTGTTGATTGGCATGCTCATAATGCTCATCCAGATGAAGCTGTTAAATAQAYGSYLHILYEDFNEPLDVSTCTTTACTAGAATTGCTCAAGCTTATGGTTCTTACTTGCATATTTTGTACGAWTDVLVPYHKKVIAAIRAIDKKAGATTTCAATGAACCATTGGATGTTTCTTGGACTGATGTTTTGGTTCCATANVIILGTPKWSQDVDVASQNPIKCCATAAAAAAGTTATTGCTGCCATTAGAGCTATTGATAAGAAGAACGTTADYQNLMYTLHFYASSHFTSDLGTTATCTTGGGTACTCCAAAATGGTCACAAGATGTTGATGTTGCTTCTCAAAAKLKTAVNNGLPVFVTEYGTCEATCCAATTAAGGATTACCAAAACTTGATGTACACTTTGCATTTTTACGCTTASGNGNLNTDSMSSWWTLLDSCATCTCATTTTACATCTGATTTGGGTGCTAAATTGAAAACTGCTGTTAACALKISYANWAISDKSEACSALSPGATGGTTTGCCAGTTTTTGTTACTGAATATGGTACTTGTGAAGCTTCTGGTATTAVNVGVSSRWTSSGNMVASATGGTAATTTGAATACTGATTCTATGTCATCTTGGTGGACTTTGTTGGATTCYYKKKSTGISCSGSSSGSSSGSSSTTTGAAAATTTCTTACGCTAATTGGGCTATTTCTGATAAATCTGAAGCTTGTGSSGTSSGSSGSSSGSSSGSSSGSTCTGCTTTGTCTCCAGGTACTACTGCTGTTAATGTTGGTGTTTCTTCTAGATSGSSSGSSSGSGSASISVVPSNTWGGACTTCTTCTGGTAATATGGTTGCTTCTTACTACAAAAAAAAGTCCACTGNGGGRVNFEIKNTGSVPLCGVVGTATTTCTTGTTCTGGTAGTTCTTCAGGTTCTTCAAGTGGTTCATCTAGTGGFSVSLPSGTTLGGSWNMESAGSTTCTTCCGGTACATCTTCTGGTTCTAGTGGTTCATCTAGTGGTAGTTCTTCCGQYSLPSWVRIEAGKSSKDAGLGGTAGTTCTAGTGGTAGTTCTGGTTCAAGTTCTGGTTCCTCCTCTGGTTCTG TFNGKDKPTAKIVTTKKC(SEQ GTTCTGCATCTATTTCTGTTGTTCCATCTAATACTTGGAATGGTGGTGGTAG ID NO: 53)AGTTAATTTTGAAATTAAGAACACTGGTTCTGTTCCATTGTGTGGTGTTGTTTTTTCTGTTTCTTTGCCATCTGGTACTACTTTGGGTGGTTCTTGGAATATGGAATCTGCTGGTTCTGGTCAATATTCTTTACCATCTTGGGTTAGAATTGAAGCTGGTAAATCTTCTAAAGATGCTGGTTTGACTTTTAATGGTAAAGATAAGCCAACTGCTAAAATTGTTACCACCAAGAAGTGCTTATAAGGCGCGCC (SEQ ID NO: 48) HypocreaTTAATTAAAATGAACAAGTCTGTTGCTCCATTGTTGTTGGCTGCTTCTATTTMNKSVAPLLLAASILYGGAVAQ jecorinaTGTATGGTGGTGCTGTTGCTCAACAAACTGTTTGGGGTCAATGTGGTGGTAQTVWGQCGGIGWSGPTNCAPGS (anamorph:TTGGTTGGTCTGGTCCAACTAATTGTGCTCCAGGTTCTGCTTGTTCTACTTTACSTLNPYYAQCIPGATTITTSTR TrichodermaGAATCCATATTATGCTCAATGTATTCCAGGTGCTACTACTATTACTACTTCTPPSGPTTTTRATSTSSSTPPTSSG reesei) Eg2ACTAGACCACCATCTGGTCCAACAACTACTACTAGAGCTACTTCTACATCTVRFAGVNIAGFDFGCTTDGTCVTCTTCTACTCCACCAACTTCATCTGGTGTTAGATTTGCTGGTGTTAACATTGTSKVYPPLKNFTGSNNYPDGIGQCTGGTTTTGATTTTGGTTGTACTACTGATGGTACTTGTGTTACTTCTAAAGTMQHFVNEDGMTIFRLPVGWQYTTACCCACCATTGAAAAATTTCACTGGTTCTAACAATTATCCAGATGGTATLVNNNLGGNLDSTSISKYDQLVTGGTCAAATGCAACATTTTGTTAACGAAGATGGTATGACTATTTTTAGATTQGCLSLGAYCIVDIHNYARWNGGCCAGTTGGTTGGCAATATTTGGTTAACAACAATTTGGGTGGTAATTTGGAGIIGQGGPTNAQFTSLWSQLASKTTCTACTTCTATTTCTAAGTACGATCAATTGGTTCAAGGTTGTTTGTCTTTGYASQSRVWFGIMNEPHDVNINTGGTGCTTACTGTATTGTTGATATTCATAATTATGCTAGATGGAATGGTGGTWAATVQEVVTAIRNAGATSQFIATTATTGGTCAAGGTGGTCCAACAAATGCTCAATTTACTTCTTTGTGGTCASLPGNDWQSAGAFISDGSAAALCAATTGGCTTCAAAATATGCTTCTCAATCTAGAGTTTGGTTTGGTATTATGSQVTNPDGSTTNLIFDVHKYLDSAATGAACCACATGATGTTAACATTAATACTTGGGCTGCTACTGTTCAAGAADNSGTHAECTTNNIDGAFSPLATGTTGTTACTGCTATTAGAAATGCTGGTGCTACTTCTCAATTCATTTCTTTGCWLRQNNRQAILTETGGGNVQSCCAGGTAATGATTGGCAATCTGCTGGTGCTTTTATTTCTGATGGTTCTGCTGCIQDMCQQIQYLNQNSDVYLGYVTGCTTTGTCTCAAGTTACTAATCCAGATGGTTCTACTACTAATTTGATCTTCGWGAGSFDSTYVLTETPTSSGNGATGTTCATAAGTACTTGGATTCTGATAATTCTGGTACTCATGCTGAATGT SWTDTSLVSSCLARK (SEQID ACTACAAACAATATTGATGGTGCTTTTTCTCCATTGGCTACTTGGTTGAGA NO: 54)CAAAACAATAGACAAGCTATTTTGACTGAAACTGGTGGTGGTAATGTTCAATCTTGTATCCAAGATATGTGCCAACAAATTCAATACTTGAACCAAAATTCTGATGTTTATTTGGGTTACGTTGGTTGGGGTGCTGGTTCTTTTGATTCTACTTACGTTTTAACTGAAACTCCAACTTCTTCTGGTAATTCTTGGACTGATACTTCTTTGGTTTCTTCATGTTTGGCTAGAAAGTTATAAGGCGCGCC (SEQ ID NO: 49) OrpinomycesTTAATTAAAATGAAGTTCTTGAACTCTTTGTCTTTGTTGGGTTTGGTTATTGMKFLNSLSLLGLVIAGCEAMRNI sp.PC-2 CelBCTGGTTGTGAAGCTATGAGAAACATTTCTTCTAAAGAATTGGTTAAAGAATSSKELVKELTIGWSLGNTLDASCTGACTATTGGTTGGTCTTTGGGTAATACTTTGGATGCTTCTTGTGTTGAAACVETLNYSKDQTASETCWGNVKTTTTGAACTACTCTAAAGATCAAACTGCTTCTGAAACTTGTTGGGGTAATGTTQELYYKLSDLGFNTFRIPTTWSTAAAACTACTCAAGAATTGTACTACAAATTGTCTGATTTGGGTTTCAATACGHFGDAPDYKISDVWMKRVHETTTCAGAATACCAACTACTTGGTCTGGTCATTTTGGTGATGCTCCAGATTAVVDYALNTGGYAILNIHHETWNCAAAATTTCTGATGTTTGGATGAAAAGAGTTCACGAAGTTGTTGATTATGCYAFQKNLESAKKILVAIWKQIATTTGAATACTGGTGGTTACGCTATTTTGAACATTCATCATGAAACTTGGAAAEFGDYDEHLIFEGMNEPRKVGTTACGCTTTTCAAAAGAATTTGGAATCTGCTAAAAAGATTTTGGTTGCTAT DPAEWTGGDQEGWNFVNEMNTTGGAAACAAATTGCTGCTGAATTTGGTGATTACGATGAACATTTGATTTTALFVKTIRATGGNNANRHLMIPTGAAGGTATGAATGAACCAAGAAAAGTTGGTGATCCAGCTGAATGGACTGTYAASVNDGSINNFKYPNGDDKGTGGTGATCAAGAAGGTTGGAATTTTGTTAATGAAATGAACGCTTTGTTCGVIVSLHSYSPYNFALNNGPGAISTTAAAACTATTAGAGCTACTGGTGGTAACAATGCTAATAGACATTTGATGANFYDGNEIDWVMNTINSSFISKGTTCCAACTTATGCTGCTTCTGTTAATGATGGTTCTATTAACAATTTTAAGTAIPVIIGEFVAMNRDNEDDRERWCCCAAATGGTGATGATAAAGTTATTGTTTCTTTGCATTCTTACTCTCCATACQEYYIKKATALGIPCVIWDNGYFAATTTTGCTTTGAACAATGGTCCAGGTGCTATTTCTAATTTCTACGATGGTEGEGERFGIIDRKSLNVIFPKLINAACGAAATTGATTGGGTTATGAACACTATTAACTCTTCATTCATTTCTAAGGLMKGLGDEKPKTTIRRTTTTTGGTATTCCAGTTATTATTGGTGAATTTGTTGCTATGAACAGAGATAATGAAVQVQPTINNECFSTRLGYSCCNGGATGATAGAGAAAGATGGCAAGAATACTACATTAAAAAGGCTACTGCTTT FDVLYTDNDGQWGVENGNWCGGGTATTCCATGTGTTATTTGGGATAATGGTTATTTTGAAGGTGAAGGTGAGIKSSCGNNQRQCWSERLGYPCAAGATTTGGTATTATTGATAGAAAGTCTTTGAACGTTATTTTCCCAAAGTTCQYTTNAEYTDNDGRWGVENG GATTAATGGTTTGATGAAAGGTTTGGGTGATGAAAAACCAAAAACTACTANWCGIY (SEQ ID NO: 55)TTAGAAGAACTACTACTACTACAGTTCAAGTTCAACCAACTATTAACAACGAATGTTTCTCTACTAGATTGGGTTATTCTTGTTGTAATGGTTTCGATGTTTTGTACACTGATAATGATGGTCAATGGGGTGTTGAAAATGGTAATTGGTGTGGTATTAAATCTTCTTGTGGTAACAATCAAAGACAATGTTGGTCTGAAAGATTAGGTTATCCATGTTGTCAATACACTACTAATGCTGAATATACAGACAACGACGGTAGATGGGGTGTAGAAAACGGTAACTGGTGCGGAATATACTTGTAA GGCGCGCC (SEQ ID NO:50) Irpex lacteus TTAATTAAAATGAAGTCTTTGTTGTTGTCTGCTGCTGCTACTTTGGCTTTATMKSLLLSAAATLALSTPAFSVSV En1CTACTCCAGCTTTTTCTGTTTCTGTTTGGGGTCAATGTGGTGGTATTGGTTTWGQCGGIGFTGSTTCDAGTSCVTACTGGTTCTACTACTTGTGATGCTGGTACTTCTTGTGTTCATTTGAACGATHLNDYYFQCQPGAATSTVQPTTTACTACTTTCAATGTCAACCAGGTGCTGCTACTTCTACTGTTCAACCAACTTASSTSSAAAPSSSGNAVCSGTRACTACTGCTTCTTCTACTTCTTCTGCTGCAGCTCCATCTTCTTCAGGTAATGNKFKFFGVNESGAEFGNNVIPGTCTGTTTGTTCTGGTACTAGAAACAAGTTTAAGTTCTTCGGTGTTAATGAATLGTDYTWPSPSSIDFFVGKGFNTCTGGTGCTGAATTTGGTAACAATGTTATTCCAGGTACTTTGGGTACTGATTFRVPFLMERLSPPATGLTGPFDSATACTTGGCCATCTCCATCTTCTATTGATTTTTTCGTTGGTAAGGGTTTTAATYLQGLKTIVSYITGKGGYALVTACTTTCAGAGTTCCATTTTTGATGGAAAGATTGTCTCCACCTGCTACTGGTDPHNFMIYNGATISDTNAFQTWTTGACTGGTCCATTTGATTCTACTTATTTGCAAGGTTTGAAAACTATTGTTTWQNLAAQFKTDSHVVFDVMNECTTACATTACTGGTAAAGGTGGTTATGCTTTGGTTGATCCACATAACTTTAPHDIPAQTVFNLNQAAINRIRASTGATTTACAACGGTGCTACTATTTCTGATACTAATGCTTTTCAAACTTGGTGGATSQSILVEGTSYTGAWTWTTGCAAAATTTGGCTGCTCAATTTAAGACTGATTCTCATGTTGTTTTCGATGTTTSGNSQVFGAIHDPNNNVAIEMATGAATGAACCACATGATATTCCAGCTCAAACTGTTTTTAACTTGAACCAAHQYLDSDGSGTSPTCVSPTIGAEGCTGCTATTAATAGAATTAGAGCTTCTGGTGCTACTTCTCAATCTATTTTGGRLQAATQWLQQNNLKGFLGEIGTTGAAGGTACTTCTTATACTGGTGCTTGGACTTGGACTACTACTTCTGGTAAGSNADCISAVQGALCEMQQSDATTCTCAAGTTTTTGGTGCTATTCATGATCCAAACAACAATGTTGCTATTG VWLGALWWAAGPWWGDYFQSAAATGCATCAATACTTGGATTCTGATGGTTCTGGTACTTCTCCAACTTGTGIEPPSGVAVSSILPQALEPFL (SEQTTTCTCCAACTATTGGTGCTGAAAGATTGCAAGCTGCTACTCAATGGTTGC ID NO: 56)AACAAAACAATTTGAAAGGTTTCTTGGGTGAAATTGGTGCTGGTTCTAATGCTGATTGTATTTCTGCTGTTCAAGGTGCTTTGTGTGAAATGCAACAATCTGATGTTTGGTTGGGTGCTTTGTGGTGGGCTGCTGGTCCATGGTGGGGTGATTATTTTCAATCTATTGAACCACCATCTGGTGTTGCTGTTTCTTCTATTTTGCCACAAGCTTTGGAACCATTTTTGTTATAAGGCGCGCC (SEQ ID NO: 51) β-GlucosidasesS.f.BGLI ATGGTCTCCTTCACCTCCCTCCTCGCCGGCGTCGCCGCCATCTCGGGCGTC FJ028723TTGGCCGCTCCCGCCGCCGAGGTCGAATCCGTGGCTGTGGAGAAGCGCTCMVSFTSLLAGVAAISGVLAAPAGGACTCGCGAGTCCCAATTCAAAACTATACCCAGTCTCCATCCCAGAGAGAEVESVAVEKRSDSRVPIQNYTATGAGAGCTCCCAATGGGTGAGCCCGCATTATTATCCAACTCCACAAGGTQSPSQRDESSQWVSPHYYPTPQGGTAGGCTCCAAGACGTCTGGCAAGAAGCATATGCTAGAGCAAAAGCCAT GGRLQDVWQEAYARAKAIVGQCGTTGGCCAGATGACTATTGTTGAAAAGGTCAATTTGACCACTGGTACCGGMTIVEKVNLTTGTGWQLDPCVGTTGGCAATTAGATCCATGTGTTGGTAATACCGGTTCTGTTCCAAGATTCGGNTGSVPRFGIPNLCLQDGPLGVRCATCCCAAACCTTTGCCTACAAGATGGGCCATTGGGTGTTCGATTCGCTGAFADFVTGYPSGLATGATFNKDLCTTTGTTACTGGCTATCCATCCGGTCTTGCTACTGGTGCAACGTTCAATAAFLQRGQALGHEFNSKGVHIALGGGATTTGTTTCTTCAAAGAGGTCAAGCTCTCGGTCATGAGTTCAACAGCAAPAVGPLGVKARGGRNFEAFGSDAGGTGTACATATTGCGTTGGGCCCTGCTGTTGGCCCACTTGGTGTCAAAGCPYLQGTAAAATIKGLQENNVMACAGAGGTGGCAGAAATTTCGAAGCCTTTGGTTCCGACCCATATCTCCAAGCVKHFIGNEQEKYRQPDDINPATGTACTGCTGCTGCTGCAACCATCAAAGGTCTCCAAGAGAATAATGTTATGNQTTKEAISANIPDRAMHELYLGCTTGTGTCAAGCACTTTATTGGTAACGAACAAGAAAAGTACAGACAGCC WPFADSVRAGVGSVMCSYNRVAGATGACATAAACCCTGCCACCAACCAAACTACTAAAGAAGCTATTAGTG NNTYACENSYMMNHLLKEELGCCAACATTCCAGACAGAGCCATGCATGAGTTGTACTTGTGGCCATTTGCCGFQGFVVSDWGAQLSGVYSAISGATTCGGTTCGAGCAGGTGTTGGTTCTGTTATGTGCTCTTATAACAGAGTCALDMSMPGEVYGGWNTGTSFWGACAACACTTACGCTTGCGAAAACTCTTACATGATGAACCACTTGCTTAAAGQNLTKAIYNETVPIERLDDMATRAAGAGTTGGGTTTTCAAGGCTTTGTTGTTTCGGACTGGGGTGCACAATTAAILAALYATNSFPTEDHLPNFSSWGTGGGGTTTATAGCGCTATCTCGGGCTTAGATATGTCTATGCCTGGTGAAGTTKEYGNKYYADNTTEIVKVNYTGTATGGGGGATGGAACACCGGCACGTCTTTCTGGGGTCAAAACTTGACGHVDPSNDFTEDTALKVAEESIVLAAAGCTATTTACAATGAGACTGTTCCGATTGAAAGATTAGATGATATGGCLKNENNTLPISPEKAKRLLLSGIAAACCAGGATCTTGGCTGCTTTGTATGCTACCAATAGTTTCCCAACAGAAGAAGPDPIGYQCEDQSCTNGALFQTCACCTTCCAAATTTTTCTTCATGGACAACGAAAGAATATGGCAATAAATAGWGSGSVGSPKYQVTPFEEISYLTTATGCTGACAACACTACCGAGATTGTCAAAGTCAACTACCATGTGGACCCARKNKMQFDYIRESYDLAQVTKATCAAATGACTTTACGGAGGACACAGCTTTGAAGGTTGCTGAGGAATCTAVASDAHLSIVVVSAASGEGYITVTTGTGCTTTTAAAAAATGAAAACAACACTTTGCCAATTTCTCCCGAAAAGGDGNQGDRRNLTLWNNGDKLIETCTAAAAGATTACTATTGTCGGGTATTGCTGCAGGCCCTGATCCGATAGGTTVAENCANTVVVVTSTGQINFEGATCAGTGTGAAGATCAATCTTGCACAAATGGCGCTTTGTTTCAAGGTTGGGFADHPNVTAIVWAGPLGDRSGTGTTCTGGCAGTGTTGGTTCTCCAAAATATCAAGTCACTCCATTTGAGGAAAAIANILFGKANPSGHLPFTIAKTDTTTCTTATCTTGCAAGAAAAAACAAGATGCAATTTGATTATATTCGGGAGTDDYIPIETYSPSSGEPEDNHLVENCTTACGACTTAGCTCAAGTTACTAAAGTAGCTTCCGATGCTCATTTGTCTADLLVDYRYFEEKNIEPRYAFGYTAGTTGTTGTCTCTGCTGCAAGCGGTGAGGGTTATATAACCGTTGACGGTAGLSYNEYEVSNAKVSAAKKVDEACCAAGGTGACAGAAGAAATCTCACTTTGTGGAACAACGGTGATAAATTGELPEPATYLSEFSYQNAKDSKNPATTGAAACAGTTGCTGAAAACTGTGCCAATACTGTTGTTGTTGTTACTTCTSDAFAPTDLNRVNEYLYPYLDSACTGGTCAAATTAATTTTGAAGGCTTTGCTGATCACCCAAATGTTACCGCANVTLKDGNYEYPDGYSTEQRTTATTGTCTGGGCCGGCCCATTAGGTGACAGATCCGGGACTGCTATCGCCAATPIQPGGGLGGNDALWEVAYKVEATTCTTTTTGGTAAAGCGAACCCATCAGGTCATCTTCCATTCACTATTGCTAVDVQNLGNSTDKFVPQLYLKHPAGACTGACGATGATTACATTCCAATTGAAACCTACAGTCCATCGAGTGGTEDGKFETPIQLRGFEKVELSPGEGAACCTGAAGACAACCACTTGGTTGAAAATGACTTGCTTGTTGACTATAGKKTVEFELLRRDLSVWDTTRQSATATTTTGAAGAGAAGAATATTGAGCCAAGATACGCATTTGGTTATGGCTTWIVESGTYEALIGVAVNDIKTSVGTCTTACAATGAGTATGAAGTTAGCAATGCAAAGGTCTCGGCAGCCAAAA LFTI (SEQ ID NO: 40)AAGTTGATGAGGAGTTGCCTGAACCAGCTACCTACTTATCGGAGTTTAGCTATCAAAATGCAAAAGACAGCAAAAATCCAAGTGATGCTTTTGCTCCAACAGATTTAAACAGAGTTAATGAGTACCTTTATCCATATTTAGATAGCAATGTTACCTTAAAAGACGGAAACTATGAGTATCCCGATGGCTACAGCACTGAGCAAAGAACAACACCTATCCAACCTGGGGGCGGCTTGGGAGGCAACGATGCTTTGTGGGAGGTCGCTTATAAAGTTGAAGTGGACGTTCAAAACTTGGGTAACTCCACTGATAAGTTTGTTCCACAGTTGTATTTGAAACACCCTGAGGATGGCAAGTTTGAAACCCCTATTCAATTGAGAGGGTTTGAAAAGGTTGAGTTGTCCCCGGGTGAGAAGAAGACAGTTGAGTTTGAGCTTTTGAGAAGAGATCTTAGTGTGTGGGATACCACCAGACAGTCTTGGATCGTTGAATCTGGTACTTATGAGGCCTTAATTGGTGTTGCTGTTAATGATATCAAGACATCTGTCCTGTTTACT ATT (SEQ ID NO: 20)

In certain aspects of the invention, the polypeptides andpolynucleotides of the present invention are provided in an isolatedform, e.g., purified to homogeneity.

The present invention also encompasses polypeptides which comprise, oralternatively consist of, an amino acid sequence which is at least about80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% similar to the polypeptide of anyof SEQ ID NOs: 21-40, 46, or 52-56 and to portions of such polypeptidewith such portion of the polypeptide generally containing at least 30amino acids and more preferably at least 50 amino acids.

As known in the art “similarity” between two polypeptides is determinedby comparing the amino acid sequence and conserved amino acidsubstitutes thereto of the polypeptide to the sequence of a secondpolypeptide.

The present invention further relates to a domain, fragment, variant,derivative, or analog of the polypeptide of any of SEQ ID NOs: 21-40,46, or 52-56.

Fragments or portions of the polypeptides of the present invention maybe employed for producing the corresponding full-length polypeptide bypeptide synthesis. Therefore, the fragments may be employed asintermediates for producing the full-length polypeptides.

Fragments of cellobiohydrolase, endoglucanase or beta-glucosidasepolypeptides encompass domains, proteolytic fragments, deletionfragments and in particular, fragments of H. grisea, T. aurantiacus, T.emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C.acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C.lucknowense, R. speratus, Thermobfida fusca, Clostridum thermocellum,Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis,Cellulomonas fimi, Saccharophagus degradans, Piromyces equii,Neocallimastix patricarum, Aspergillus kawachii, Heterodera schachtii,H. jecorina, Orpinomyces sp., Irpex lacteus, Acremonium thermophilum,Neosartorya fischeri, Chaetomium globosum, Chaetomium thermophilum,Aspergillus fumigatus, Aspergillus terreus, Neurospora Crassa, R.flavipes, or Arabidopsis thaliana cellobiohydrolase, endoglucanase orbeta-glucosidase polypeptides which retain any specific biologicalactivity of the cellobiohydrolase, endoglucanase or beta-glucosidaseproteins. Polypeptide fragments further include any portion of thepolypeptide which retains a catalytic activity of cellobiohydrolase,endoglucanase or beta-glucosidase proteins.

The variant, derivative or analog of the polypeptide of any of SEQ IDNOs: 21-40, 46, or 52-56, may be (i) one in which one or more of theamino acid residues are substituted with a conserved or non-conservedamino acid residue (preferably a conserved amino acid residue) and suchsubstituted amino acid residue may or may not be one encoded by thegenetic code, or (ii) one in which one or more of the amino acidresidues includes a substituent group, or (iii) one in which the maturepolypeptide is fused with another compound, such as a compound toincrease the half-life of the polypeptide (for example, polyethyleneglycol), or (iv) one in which the additional amino acids are fused tothe mature polypeptide for purification of the polypeptide or (v) one inwhich a fragment of the polypeptide is soluble, i.e., not membranebound, yet still binds ligands to the membrane bound receptor. Suchvariants, derivatives and analogs are deemed to be within the scope ofthose skilled in the art from the teachings herein.

The polypeptides of the present invention further include variants ofthe polypeptides. A “variant” of the polypeptide can be a conservativevariant, or an allelic variant. As used herein, a conservative variantrefers to alterations in the amino acid sequence that do not adverselyaffect the biological functions of the protein. A substitution,insertion or deletion is said to adversely affect the protein when thealtered sequence prevents or disrupts a biological function associatedwith the protein. For example, the overall charge, structure orhydrophobic-hydrophilic properties of the protein can be altered withoutadversely affecting a biological activity. Accordingly, the amino acidsequence can be altered, for example to render the peptide morehydrophobic or hydrophilic, without adversely affecting the biologicalactivities of the protein.

By an “allelic variant” is intended alternate forms of a gene occupyinga given locus on a chromosome of an organism. Genes II, Lewin, B., ed.,John Wiley & Sons, New York (1985). Non-naturally occurring variants maybe produced using art-known mutagenesis techniques. Allelic variants,though possessing a slightly different amino acid sequence than thoserecited above, will still have the same or similar biological functionsassociated with the H. grisea, T. aurantiacus, T. emersonii, T. reesei,C. lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M.darwinensis, N. walkeri, S. fibuligera, C. lucknowense, R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, R. flavipes, or Arabidopsis thalianacellobiohydrolase, endoglucanase or beta-glucosidase protein.

The allelic variants, the conservative substitution variants, andmembers of the endoglucanase, cellobiohydrolase or β-glucosidase proteinfamilies, can have an amino acid sequence having at least 75%, at least80%, at least 90%, at least 95% amino acid sequence identity with a H.grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C.formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, S. fibuligera, C. lucknowense, R. speratus, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, R. flavipes, or Neosartorya fischericellobiohydrolase, endoglucanase or beta-glucosidase amino acid sequenceset forth in any one of SEQ ID NOs: 21-40, 46, or 52-56. Identity orhomology with respect to such sequences is defined herein as thepercentage of amino acid residues in the candidate sequence that areidentical with the known peptides, after aligning the sequences andintroducing gaps, if necessary, to achieve the maximum percent homology,and not considering any conservative substitutions as part of thesequence identity. N-terminal, C-terminal or internal extensions,deletions, or insertions into the peptide sequence shall not beconstrued as affecting homology.

Thus, the proteins and peptides of the present invention includemolecules comprising the amino acid sequence of SEQ ID NOs: 21-40, 46and 52-56 or fragments thereof having a consecutive sequence of at leastabout 3, 4, 5, 6, 10, 15, 20, 25, 30, 35 or more amino acid residues ofthe H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C.formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, S. fibuligera, C. lucknowense, R. speratus, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, R. flavipes, or Neosartorya fischericellobiohydrolase, endoglucanase or beta-glucosidase polypeptidesequences; amino acid sequence variants of such sequences wherein atleast one amino acid residue has been inserted N- or C-terminal to, orwithin, the disclosed sequence; amino acid sequence variants of thedisclosed sequences, or their fragments as defined above, that have beensubstituted by another residue. Contemplated variants further includethose containing predetermined mutations by, e.g., homologousrecombination, site-directed or PCR mutagenesis, and the correspondingproteins of other animal species, including but not limited tobacterial, fungal, insect, rabbit, rat, porcine, bovine, ovine, equineand non-human primate species, the alleles or other naturally occurringvariants of the family of proteins; and derivatives wherein the proteinhas been covalently modified by substitution, chemical, enzymatic, orother appropriate means with a moiety other than a naturally occurringamino acid (for example, a detectable moiety such as an enzyme orradioisotope).

Using known methods of protein engineering and recombinant DNAtechnology, variants may be generated to improve or alter thecharacteristics of the cellulase polypeptides. For instance, one or moreamino acids can be deleted from the N-terminus or C-terminus of thesecreted protein without substantial loss of biological function.

Thus, the invention further includes H. grisea, T. aurantiacus, T.emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C.acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C.lucknowense, R. speratus, Thermobfida fusca, Clostridum thermocellum,Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis,Cellulomonas fimi, Saccharophagus degradans, Piromyces equii,Neocallimastix patricarum, Aspergillus kawachii, Heterodera schachtii,H. jecorina, Orpinomyces sp., Irpex lacteus, Acremonium thermophilum,Neosartorya fischeri, Chaetomium globosum, Chaetomium thermophilum,Aspergillus fumigatus, Aspergillus terreus, Neurospora Crassa, R.flavipes or Arabidopsis thaliana cellobiohydrolase, endoglucanase orbeta-glucosidase polypeptide variants which show substantial biologicalactivity. Such variants include deletions, insertions, inversions,repeats, and substitutions selected according to general rules known inthe art so as have little effect on activity.

The skilled artisan is fully aware of amino acid substitutions that areeither less likely or not likely to significantly effect proteinfunction (e.g., replacing one aliphatic amino acid with a secondaliphatic amino acid), as further described below.

For example, guidance concerning how to make phenotypically silent aminoacid substitutions is provided in Bowie et al., “Deciphering the Messagein Protein Sequences: Tolerance to Amino Acid Substitutions,” Science247:1306-1310 (1990), wherein the authors indicate that there are twomain strategies for studying the tolerance of an amino acid sequence tochange.

The first strategy exploits the tolerance of amino acid substitutions bynatural selection during the process of evolution. By comparing aminoacid sequences in different species, conserved amino acids can beidentified. These conserved amino acids are likely important for proteinfunction. In contrast, the amino acid positions where substitutions havebeen tolerated by natural selection indicates that these positions arenot critical for protein function. Thus, positions tolerating amino acidsubstitution could be modified while still maintaining biologicalactivity of the protein.

The second strategy uses genetic engineering to introduce amino acidchanges at specific positions of a cloned gene to identify regionscritical for protein function. For example, site directed mutagenesis oralanine-scanning mutagenesis (introduction of single alanine mutationsat every residue in the molecule) can be used. (Cunningham and Wells,Science 244:1081-1085 (1989).) The resulting mutant molecules can thenbe tested for biological activity.

As the authors state, these two strategies have revealed that proteinsare often surprisingly tolerant of amino acid substitutions. The authorsfurther indicate which amino acid changes are likely to be permissive atcertain amino acid positions in the protein. For example, most buried(within the tertiary structure of the protein) amino acid residuesrequire nonpolar side chains, whereas few features of surface sidechains are generally conserved. Moreover, tolerated conservative aminoacid substitutions involve replacement of the aliphatic or hydrophobicamino acids Ala, Val, Leu and Ile; replacement of the hydroxyl residuesSer and Thr; replacement of the acidic residues Asp and Glu; replacementof the amide residues Asn and Gln, replacement of the basic residuesLys, Arg, and His; replacement of the aromatic residues Phe, Tyr, andTrp, and replacement of the small-sized amino acids Ala, Ser, Thr, Met,and Gly.

The terms “derivative” and “analog” refer to a polypeptide differingfrom the H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus,C. formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, S. fibuligera, C. lucknowense, R. speratus, Thermobfida fusca,Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui,Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromycesequii, Neocallimastix patricarum, Aspergillus kawachii, Heteroderaschachtii, H. jecorina, Orpinomyces sp., Irpex lacteus, Acremoniumthermophilum, Neosartorya fischeri, Chaetomium globosum, Chaetomiumthermophilum, Aspergillus fumigatus, Aspergillus terreus, NeurosporaCrassa, R. flavipes, or Arabidopsis thaliana cellobiohydrolase,endoglucanase or beta-glucosidase polypeptide, but retaining essentialproperties thereof. Generally, derivatives and analogs are overallclosely similar, and, in many regions, identical to the H. grisea, T.aurantiacus, T. emersonii, T. reesei, C. lacteus, C. formosanus, N.takasagoensis, C. acinaciformis, M. darwinensis, N. walkeri, S.fibuligera, C. lucknowense, R. speratus, Thermobfida fusca, Clostridumthermocellum, Clostridium cellulolyticum, Clostridum josui, Bacilluspumilis, Cellulomonas fimi, Saccharophagus degradans, Piromyces equii,Neocallimastix patricarum, Aspergillus kawachii, Heterodera schachtii,H. jecorina, Orpinomyces sp., Irpex lacteus, Acremonium thermophilum,Neosartorya fischeri, Chaetomium globosum, Chaetomium thermophilum,Aspergillus fumigatus, Aspergillus terreus, Neurospora Crassa, R.flavipes, or Arabidopsis thaliana cellobiohydrolase, endoglucanase orbeta-glucosidase polypeptides. The terms “derivative” and “analog” whenreferring to H. grisea, T. aurantiacus, T. emersonii, T. reesei, C.lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M.darwinensis, N. walkeri, S. fibuligera, C. lucknowense, R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, R. flavipes or Arabidopsis thalianacellobiohydrolase, endoglucanase or beta-glucosidase polypeptidesinclude any polypeptides which retain at least some of the activity ofthe corresponding native polypeptide, e.g., the exoglucanase activity,or the activity of the catalytic domain.

Derivatives of H. grisea, T. aurantiacus, T. emersonii, T. reesei, C.lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M.darwinensis, N. walkeri, S. fibuligera, C. lucknowense, R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, R. flavipes, or Arabidopsis thalianacellobiohydrolase, endoglucanase or beta-glucosidase polypeptides, arepolypeptides which have been altered so as to exhibit additionalfeatures not found on the native polypeptide. Derivatives can becovalently modified by substitution, chemical, enzymatic, or otherappropriate means with a moiety other than a naturally occurring aminoacid (for example, a detectable moiety such as an enzyme orradioisotope). Examples of derivatives include fusion proteins.

An analog is another form of a H. grisea, T. aurantiacus, T. emersonii,T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C.acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C.lucknowense, R. speratus, Thermobfida fusca, Clostridum thermocellum,Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis,Cellulomonas fimi, Saccharophagus degradans, Piromyces equii,Neocallimastix patricarum, Aspergillus kawachii, Heterodera schachtii,H. jecorina, Orpinomyces sp., Irpex lacteus, Acremonium thermophilum,Neosartorya fischeri, Chaetomium globosum, Chaetomium thermophilum,Aspergillus fumigatus, Aspergillus terreus, Neurospora Crassa, R.flavipes, or Arabidopsis thaliana cellobiohydrolase, endoglucanase orbeta-glucosidase polypeptide of the present invention. An “analog” alsoretains substantially the same biological function or activity as thepolypeptide of interest, e.g., functions as a cellobiohydrolase. Ananalog includes a proprotein which can be activated by cleavage of theproprotein portion to produce an active mature polypeptide.

The polypeptide of the present invention may be a recombinantpolypeptide, a natural polypeptide or a synthetic polypeptide. In someparticular embodiments, the polypeptide is a recombinant polypeptide.

Also provided in the present invention are allelic variants, orthologs,and/or species homologs. Procedures known in the art can be used toobtain full-length genes, allelic variants, splice variants, full-lengthcoding portions, orthologs, and/or species homologs of genescorresponding to any of SEQ ID NOs: 1-40, using information from thesequences disclosed herein or the clones deposited with the ATCC. Forexample, allelic variants and/or species homologs may be isolated andidentified by making suitable probes or primers from the sequencesprovided herein and screening a suitable nucleic acid source for allelicvariants and/or the desired homologue.

Consensus Sequence Cellulases

In some embodiments of the present invention, the host cells express atleast one heterologous cellulase that is not derived from any oneparticular organism, but instead has an artificial amino acid sequencethat is a consensus cellulase sequence. The consensus cellulase sequencecan be an endoglucanase consensus sequence, a β-glucosidase consensussequence, or a cellobiohydrolase consensus sequence.

In one particular embodiment, the heterologous cellulase is a CBH1consensus sequence. Therefore, in one embodiment, the invention isdirected to a polypeptide sequence which comprises a sequence that is atleast 80%, 85%, 90%, 95%, 98% or 99% identical to the consensus CBH1sequence of SEQ ID NO: 43. In some embodiments, the invention isdirected to a polypeptide which comprises the sequence of SEQ ID NO: 43.

The invention is also directed to host cells that comprise a polypeptidesequence which comprises a sequence that is at least 80%, 85%, 90%, 95%,98% 99% or 100% identical to the consensus CBH1 sequence of SEQ ID NO:43. The invention further directed to host cells that comprise apolynucleotide that encodes a polypeptide sequence which comprises asequence that is at least 80%, 85%, 90%, 95%, 98% 99% or 100% identicalto the consensus CBH1 sequence of SEQ ID NO: 43. In some embodiments thehost cell comprises at least one polynucleotide that encodes apolypeptide sequence which comprises a sequence that is at least 80%,85%, 90%, 95%, 98%, 99% or 100% identical to the consensus CBH1 sequenceof SEQ ID NO: 43 and at least a second polynucleotide that encodes aheterologous cellulase. The second polynucleotide can encode aendoglucanase, a β-glucosidase, a cellobiohydrolase, an endoglucanaseconsensus sequence, a β-glucosidase consensus sequence, or acellobiohydrolase consensus sequence. In some embodiments the host cellcomprising the polynucleotide that encodes a polypeptide sequence whichcomprises a sequence that is at least 80%, 85%, 90%, 95%, 98%, 99%, or100% identical to the consensus CBH1 sequence of SEQ ID NO: 43 iscapable of producing ethanol when grown using cellulose as a carbonsource.

Combinations of Cellulases

In some embodiments of the present invention the host cells express acombination of heterologous cellulases. For example, the host cell cancontain at least two heterologous cellulases, at least threeheterologous cellulases, at least four heterologous cellulases, at leastfive heterologous cellulases, at least six heterologous cellulases, atleast seven heterologous cellulases, at least eight heterologouscellulases, at least nine heterologous cellulases, at least tenheterologous cellulases, at least eleven heterologous cellulases, atleast twelve heterologous cellulases, at least thirteen heterologouscellulases, at least fourteen heterologous cellulases or at leastfifteen heterologous cellulases. The heterologous cellulases in the hostcell can be from the same or from different species.

In some embodiments of the present invention, the host cells express acombination of heterologous cellulases which includes at least oneendoglucanase, at least one β-glucosidase and at least onecellobiohydrolase. In another embodiment of the invention, the hostcells express a combination of heterologous cellulases which includes atleast one endoglucanase, at least one β-glucosidase and at least twocellobiohydrolases. The at least two cellobiohydrolases can be both becellobiohydrolase I, can both be cellobiohydrolase II, or can be onecellobiohydrolase I and one cellobiohydrolase II.

In one particular embodiment of the invention, the host cells express acombination of cellulases that includes a C. formosanus endoglucanase Iand an S. fibuligera β-glucosidase I. In another embodiment of theinvention, the host cells express a combination of cellulases thatincludes a T. emersonii cellobiohydrolase I, and a T. reeseicellobiohydrolase II.

In yet another embodiment the host cells express a combination ofcellulases that includes a C. formosanus endoglucanase I, an S.fibuligera β-glucosidase I, a T. emersonii cellobiohydrolase I, and a C.lucknowense cellobiohydrolase IIb. In still another embodiment, the hostcells express a combination of cellulases that includes a C. formosanusendoglucanase I, an S. fibuligera β-glucosidase I, a T. emersoniicellobiohydrolase I, and a T. reesei cellobiohydrolase II. In stillanother embodiment, the host cells express a combination of cellulasesthat includes an H. jecorina endogluconase 2, an S. fibuligeraβ-glucosidase I, a T. emersonii cellobiohydrolase I, and a T. reeseicellobiohydrolase II. In still another embodiment, the host cellsexpress a combination of cellulases that includes an H. jecorinaendogluconase 2, an S. fibuligera β-glucosidase I, a T. emersoniicellobiohydrolase I, and a C. lucknowense cellobiohydrolase II.

Tethered and Secreted Cellulases

According to the present invention, the cellulases may be eithertethered or secreted. As used herein, a protein is “tethered” to anorganism's cell surface if at least one terminus of the protein isbound, covalently and/or electrostatically for example, to the cellmembrane or cell wall. It will be appreciated that a tethered proteinmay include one or more enzymatic regions that may be joined to one ormore other types of regions at the nucleic acid and/or protein levels(e.g., a promoter, a terminator, an anchoring domain, a linker, asignaling region, etc.). While the one or more enzymatic regions may notbe directly bound to the cell membrane or cell wall (e.g., such as whenbinding occurs via an anchoring domain), the protein is nonethelessconsidered a “tethered enzyme” according to the present specification.

Tethering may, for example, be accomplished by incorporation of ananchoring domain into a recombinant protein that is heterologouslyexpressed by a cell, or by prenylation, fatty acyl linkage, glycosylphosphatidyl inositol anchors or other suitable molecular anchors whichmay anchor the tethered protein to the cell membrane or cell wall of thehost cell. A tethered protein maybe tethered at its amino terminal endor optionally at its carboxy terminal end.

As used herein, “secreted” means released into the extracellular milieu,for example into the media. Although tethered proteins may havesecretion signals as part of their immature amino acid sequence, theyare maintained as attached to the cell surface, and do not fall withinthe scope of secreted proteins as used herein.

As used herein, “flexible linker sequence” refers to an amino acidsequence which links two amino acid sequences, for example, a cell wallanchoring amino acid sequence with an amino acid sequence that containsthe desired enzymatic activity. The flexible linker sequence allows fornecessary freedom for the amino acid sequence that contains the desiredenzymatic activity to have reduced steric hindrance with respect toproximity to the cell and may also facilitate proper folding of theamino acid sequence that contains the desired enzymatic activity.

In some embodiments of the present invention, the tethered cellulaseenzymes are tethered by a flexible linker sequence linked to ananchoring domain. In some embodiments, the anchoring domain is of CWP2(for carboxy terminal anchoring) or FLO1 (for amino terminal anchoring)from S. cerevisiae.

In some embodiments, heterologous secretion signals may be added to theexpression vectors of the present invention to facilitate theextra-cellular expression of cellulase proteins. In some embodiments,the heterologous secretion signal is the secretion signal from T. reeseiXyn2.

Fusion Proteins Comprising Cellulases

The present invention also encompasses fusion proteins. For example, thefusion proteins can be a fusion of a heterologous cellulase and a secondpeptide. The heterologous cellulase and the second peptide can be fuseddirectly or indirectly, for example, through a linker sequence. Thefusion protein can comprise for example, a second peptide that isN-terminal to the heterologous cellulase and/or a second peptide that isC-terminal to the heterologous cellulase. Thus, in certain embodiments,the polypeptide of the present invention comprises a first polypeptideand a second polypeptide, wherein the first polypeptide comprises aheterologous cellulase.

According to the present invention, the fusion protein can comprise afirst and second polypeptide wherein the first polypeptide comprises aheterologous cellulase and the second polypeptide comprises a signalsequence. According to another embodiment, the fusion protein cancomprise a first and second polypeptide, wherein the first polypeptidecomprises a heterologous cellulase and the second polypeptide comprisesa polypeptide used to facilitate purification or identification or areporter peptide. The polypeptide used to facilitate purification oridentification or the reporter peptide can be, for example, a HIS-tag, aGST-tag, an HA-tag, a FLAG-tag, a MYC-tag, or a fluorescent protein.

According to yet another embodiment, the fusion protein can comprise afirst and second polypeptide, wherein the first polypeptide comprises aheterologous cellulase and the second polypeptide comprises an anchoringpeptide. In some embodiments, the anchoring domain is of CWP2 (forcarboxy terminal anchoring) or FLO1 (for amino terminal anchoring) fromS. cerevisiae.

According to yet another embodiment, the fusion protein can comprise afirst and second polypeptide, wherein the first polypeptide comprises aheterologous cellulase and the second polypeptide comprises a cellulosebinding module (CBM). In some embodiments, the CBM is from, for example,T. reesei Cbh1 or Cbh2, from H. grisea Cbh1, or from C. lucknowenseCbh2b. In some particular embodiments, the CBM is fused to acellobiohydrolase. In one particular embodiment, the fusion proteincomprises a first and second polypeptide, wherein the first polypeptidecomprises a heterologous cellobiohydrolase and the second polypeptidecomprises a CBM. In yet another particular embodiment, thecellobiohydrolase is T. emersonii cellobiohydrolase I and the CBM is aT. reesei cellobiohydrolase CBM. In yet another particular embodiment,the cellobiohydrolase is T. emersonii cellobiohydrolase I and the CBM isa H. grisea cellobiohydrolase CBM. In some embodiments, the CBM of H.grisea comprises amino acids 492-525 of SEQ ID NO: 21.

In certain embodiments, the polypeptide of the present inventionencompasses a fusion protein comprising a first polypeptide and a secondpolypeptide, wherein the first polypeptide is a cellobiohydrolase, andthe second polypeptide is a domain or fragment of a cellobiohydrolase.In certain embodiments, the polypeptide of the present inventionencompasses a fusion protein comprising a first polypeptide, where thefirst polypeptide is a T. emersonii Cbh1, H. grisea Cbh1, T.aurantiacusi Cbh1, T. emersonii Cbh2, T. reesei Cbh1 T. reesei Cbh2, C.lucknowense Cbh2b, or domain, fragment, variant, or derivative thereof,and a second polypeptide, where the second polypeptide is a T. emersoniiCbh1, H. grisea Cbh1, or T. aurantiacusi Cbh1, T. emersonii Cbh2, T.reesei Cbh1 or T. reesei Cbh2, C. lucknowense Cbh2b, or domain,fragment, variant, or derivative thereof. In particular embodiments thefirst polypeptide is T. emersonii Cbh1 and the second polynucleotide isa CBM from T. reesei Cbh1 or Cbh2 or from C. lucknowense Cbh2b. Inadditional embodiments, the first polypeptide is either N-terminal orC-terminal to the second polypeptide. In certain other embodiments, thefirst polypeptide and/or the second polypeptide are encoded bycodon-optimized polynucleotides, for example, polynucleotidescodon-optimized for S. cerevisiae or Kluveromyces. In particularembodiments, the first polynucleotide is a codon-optimized T. emersoniicbh1 and the second polynucleotide encodes for a codon-optimized CBMfrom T. reesei Cbh1 or Cbh2. In another particular embodiments, thefirst polynucleotide is a codon-optimized T. emersonii cbh1 and thesecond polynucleotide encodes for a codon-optimized CBM from C.lucknowense or Cbh2b.

In certain other embodiments, the first polypeptide and the secondpolypeptide are fused via a linker sequence. The linker sequence can, insome embodiments, be encoded by a codon-optimized polynucelotide.(Codon-optimized polynucleotides are described in more detail below.) Anamino acid sequence corresponding to a codon-optimized linker 1according to the invention is a flexible linker—strep tag—TEVsite—FLAG—flexible linker fusion and corresponds to GGGGSGGGGS AWHPQFGGENLYFQG DYKDDDK GGGGSGGGGS (SEQ ID NO:57)

The DNA sequence is as follows:

(SEQ ID NO: 41) GGAGGAGGTGGTTCAGGAGGTGGTGGGTCTGCTTGGCATCCACAATTTGGAGGAGGCGGTGGTGAAAATCTGTATTTCCAGGGAGGCGGAGGTGATTACAAGGATGACGACAAAGG AGGTGGTGGATCAGGAGGTGGTGGCTCC

An amino acid sequence corresponding to optimized linker 2 is a flexiblelinker—strep tag—linker—TEV site— flexible linker and corresponds toGGGGSGGGGS WSHPQFEK GG ENLYFQG GGGGSGGGGS (SEQ ID NO:58). The DNAsequence is as follows:

(SEQ ID NO: 42) ggtggcggtggatctggaggaggcggttcttggtctcacccacaatttgaaaagggtggagaaaacttgtactttcaaggcggtggtggaggttctg gcggaggtggctccggctca

Co-Cultures

The present invention is also directed to co-cultures comprising atleast two yeast host cells wherein the at least two yeast host cellseach comprise an isolated polynucleotide encoding a heterologouscellulase. As used herein, “co-culture” refers to growing two differentstrains or species of host cells together in the same vessel. In someembodiments of the invention, at least one host cell of the co-culturecomprises a heterologous polynucleotide comprising a nucleic acid whichencodes an endoglucanase, at least one host cell of the co-culturecomprises a heterologous polynucleotide comprising a nucleic acid whichencodes a β-glucosidase and at least one host cell comprises aheterologous polynucleotide comprising a nucleic acid which encodes acellobiohydrolase. In a further embodiment, the co-culture furthercomprises a host cell comprising a heterologous polynucleotidecomprising a nucleic acid which encodes a second cellobiohydrolase.

The co-culture can comprise two or more strains of yeast host cells andthe heterologous cellulases can be expressed in any combination in thetwo or more strains of host cells. For example, according to the presentinvention, the co-culture can comprise two strains: one strain of hostcells that expresses an endoglucanase and a second strain of host cellsthat expresses a β-glucosidase, a cellobiohydrolase and a secondcellobiohydrolase. According to the present invention, the co-culturecan also comprise four strains: one strain of host cells which expressesan endoglucanase, one strain of host cells that expresses aβ-glucosidase, one strain of host cells which expresses a firstcellobiohydrolase, and one strain of host cells which expressess asecond cellobiohydrolase. Similarly, the co-culture can comprise onestrain of host cells that expresses two cellulases, for example anendoglucanase and a beta-glucosidase and a second strain of host cellsthat expresses one or more cellulases, for example one or morecellobiohydrolases. The co-culture can, in addition to the at least twohost cells comprising heterologous cellulases, also include other hostcells which do not comprise heterologous cellulases.

The various host cell strains in the co-culture can be present in equalnumbers, or one strain or species of host cell can significantlyoutnumber another second strain or species of host cells. For example,in a co-culture comprising two strains or species of host cells theratio of one host cell to another can be about 1:1, 1:2, 1:3, 1:4, 1:5,1:10, 1:100, 1:500 or 1:1000. Similarly, in a co-culture comprisingthree or more strains or species of host cells, the strains or speciesof host cells may be present in equal or unequal numbers.

The co-cultures of the present invention can include tetheredcellulases, secreted cellulases or both tethered and secretedcellulases. For example, in some embodiments of the invention, theco-culture comprises at least one yeast host cell comprising apolynucleotide encoding a secreted heterologous cellulase. In anotherembodiment, the co-culture comprises at least one yeast host cellcomprising a polynucleotide encoding a tethered heterologous cellulase.In one embodiment, all of the heterologous cellulases in the co-cultureare secreted, and in another embodiment, all of the heterologouscellulases in the co-culture are tethered. In addition, othercellulases, such as externally added cellulases may be present in theco-culture.

Polynucleotides Encoding Heterologous Cellulases

The present invention also includes isolated polynucleotides encodingcellulases of the present invention. Thus, the polynucleotides of theinvention can encode endoglucanases or exoglucanases. Thepolynucleotides can encode endoglucanases, β-glucosidases orcellobiohydrolases.

In some particular embodiments of the invention, the polynucleotideencodes an endoglucanase which is an endo-1,4-β-glucanase. In particularembodiments, the polynucleotide encodes an endoglucanase I fromTrichoderma reesei. In certain other embodiments, the endoglucanase isencoded by a polynucleotide comprising a sequence at least about 70,about 80, about 90, about 95, about 96, about 97, about 98, about 99, or100% identical to SEQ ID NO:19. In particular embodiments, thepolynucleotide encodes an endoglucanase I from C. formosanus. In certainother embodiments, the endoglucanase is encoded by a polynucleotidecomprising a sequence at least about 70, about 80, about 90, about 95,about 96, about 97, about 98, about 99, or 100% identical to SEQ IDNO:11. In particular embodiments, the polynucleotide encodes anendoglucanase I from Trichoderma reesei. In certain other embodiments,the endoglucanase is encoded by a polynucleotide comprising a sequenceat least about 70, about 80, about 90, about 95, about 96, about 97,about 98, about 99, or 100% identical to SEQ ID NO:19. In particularembodiments, the polynucleotide encodes an endoglucanase 2 from H.jecorina. In certain other embodiments, the endoglucanase is encoded bya polynucleotide comprising a sequence at least about 70, about 80,about 90, about 95, about 96, about 97, about 98, about 99, or 100%identical to SEQ ID NO:54.

In certain embodiments, the polynucleotide encodes a β-glucosidase I ora β-glucosidase II isoform, paralogue or orthologue. In certainembodiments of the present invention the polynucleotide encodes aβ-glucosidase derived from Saccharomycopsis fibuligera. In particularembodiments, the β-glucosidase is encoded by a polynucleotide comprisinga sequence at least about 70, about 80, about 90, about 95, about 96,about 97, about 98, about 99, or 100% identical to SEQ ID NO:20.

In certain embodiments of the invention, the polynucleotide encodes acellobiohydrolase I and/or an cellobiohydrolase II isoform, paralogue ororthologue. In particular embodiments of the present invention, thepolynucleotide encodes the cellobiohydrolase I or II from Trichodermareesei. In particular embodiments of the present invention, thepolynucleotide encodes the cellobiohydrolase I or II from Trichodermaemersonii. In another embodiment, the cellobiohydrolase is encoded by apolynucleotide comprising a sequence at least about 70, about 80, about90, about 95, about 96, about 97, about 98, about 99, or 100% identicalto SEQ ID NO:7 or SEQ ID NO:8. In particular embodiments of the presentinvention, the polynucleotide encodes a cellobiohydrolase from C.lucknowense. In another embodiment, the cellobiohydrolase is encoded bya polynucleotide comprising a sequence at least about 70, about 80,about 90, about 95, about 96, about 97, about 98, about 99, or 100%identical to SEQ ID NO:5.

In further embodiments the polynucleotide is a polypeptide comprising asequence at least about 70, about 80, about 90, about 95, about 96,about 97, about 98, about 99, or 100% identical to a nucleotide sequencelisted in Table 1. In certain aspects the polynucleotide can encode anendoglucanase, cellobiohydrolase or β-glucosidase derived from, forexample, a fungal, bacterial, protozoan or termite source.

In certain aspects, the present invention relates to a polynucleotidecomprising a nucleic acid encoding a functional or structural domain ofT. emersonii, H. grisea, T. aurantiacus, C. lucknowense or T. reeseiCbh1 or Cbh2. For example, the domains of T. reesei Cbh1 include,without limitation: (1) a signal sequence, from amino acid 1 to 33 ofSEQ ID NO: 27; (2) a catalytic domain (CD) from about amino acid 41 toabout amino acid 465 of SEQ ID NO: 27; and (3) a cellulose bindingmodule (CBM) from about amino acid 503 to about amino acid 535 of SEQ IDNO: 27. The domains of T. reesei Cbh2 include, without limitation: (1) asignal sequence, from amino acid 1 to 33 of SEQ ID NO: 27; (2) acatalytic domain (CD) from about amino acid 145 to about amino acid 458of SEQ ID NO: 27; and (3) a cellulose binding module (CBM) from aboutamino acid 52 to about amino acid 83 of SEQ ID NO: 27.

The present invention also encompasses an isolated polynucleotidecomprising a nucleic acid that is at least about 70%, 75%, or 80%identical, at least about 90% to about 95% identical, or at least about96%, 97%, 98%, 99% or 100% identical to a nucleic acid encoding a T.emersonii, H. grisea, T. aurantiacus, C. lucknowense or T. reesei Cbh1or Cbh2 domain, as described above.

The present invention also encompasses variants of the cellulase genes,as described above. Variants may contain alterations in the codingregions, non-coding regions, or both. Examples are polynucleotidevariants containing alterations which produce silent substitutions,additions, or deletions, but do not alter the properties or activitiesof the encoded polypeptide. In certain embodiments, nucleotide variantsare produced by silent substitutions due to the degeneracy of thegenetic code. In further embodiments, H. grisea, T. aurantiacus, T.emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C.acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C. luckowenseR. speratus, Thermobfida fusca, Clostridum thermocellum, Clostridiumcellulolyticum, Clostridum josui, Bacillus pumilis, Cellulomonas fimi,Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum,Aspergillus kawachii, Heterodera schachtii, H. jecorina, Orpinomycessp., Irpex lacteus, Acremonium thermophilum, Neosartorya fischeri,Chaetomium globosum, Chaetomium thermophilum, Aspergillus fumigatus,Aspergillus terreus, Neurospora Crassa, R. flavipes, and Arabidopsisthaliana cellulase polynucleotide variants can be produced for a varietyof reasons, e.g., to optimize codon expression for a particular host.Codon-optimized polynucleotides of the present invention are discussedfurther below.

The present invention also encompasses an isolated polynucleotideencoding a fusion protein. In certain embodiments, the nucleic acidencoding a fusion protein comprises a first polynucleotide encoding fora T. emersonii cbh1, H. grisea cbh1, T. aurantiacusi cbh1 or T.emersonii cbh1 and a second polynucleotide encoding for the CBM domainof T. reesei cbh1 or T. reesei cbh2 or C. lucknowense cbh2b. Inparticular embodiments of the nucleic acid encoding a fusion protein,the first polynucleotide encodes T. emersonii cbh1 and the secondpolynucleotide encodes for a CBM from T. reesei Cbh1 or Cbh2.

In further embodiments, the first and second polynucleotides are in thesame orientation, or the second polynucleotide is in the reverseorientation of the first polynucleotide. In additional embodiments, thefirst polynucleotide encodes a polypeptide that is either N-terminal orC-terminal to the polypeptide encoded by the second polynucleotide. Incertain other embodiments, the first polynucleotide and/or the secondpolynucleotide are encoded by codon-optimized polynucleotides, forexample, polynucleotides codon-optimized for S. cerevisiae,Kluyveromyces or for both S. cerevisiae and Kluyveromyces. In particularembodiments of the nucleic acid encoding a fusion protein, the firstpolynucleotide is a codon-optimized T. emersonii cbh1 and the secondpolynucleotide encodes for a codon-optimized CBM from T. reesei Cbh1 orCbh2.

Also provided in the present invention are allelic variants, orthologs,and/or species homologs. Procedures known in the art can be used toobtain full-length genes, allelic variants, splice variants, full-lengthcoding portions, orthologs, and/or species homologs of genescorresponding to any of SEQ ID NOs: 1-20, using information from thesequences disclosed herein or the clones deposited with the ATCC. Forexample, allelic variants and/or species homologs may be isolated andidentified by making suitable probes or primers from the sequencesprovided herein and screening a suitable nucleic acid source for allelicvariants and/or the desired homologue.

By a nucleic acid having a nucleotide sequence at least, for example,95% “identical” to a reference nucleotide sequence of the presentinvention, it is intended that the nucleotide sequence of the nucleicacid is identical to the reference sequence except that the nucleotidesequence may include up to five point mutations per each 100 nucleotidesof the reference nucleotide sequence encoding the particularpolypeptide. In other words, to obtain a nucleic acid having anucleotide sequence at least 95% identical to a reference nucleotidesequence, up to 5% of the nucleotides in the reference sequence may bedeleted or substituted with another nucleotide, or a number ofnucleotides up to 5% of the total nucleotides in the reference sequencemay be inserted into the reference sequence. The query sequence may bean entire sequence shown of any of SEQ ID NOs:1-20, or any fragment ordomain specified as described herein.

As a practical matter, whether any particular nucleic acid molecule orpolypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99%identical to a nucleotide sequence or polypeptide of the presentinvention can be determined conventionally using known computerprograms. A method for determining the best overall match between aquery sequence (a sequence of the present invention) and a subjectsequence, also referred to as a global sequence alignment, can bedetermined using the FASTDB computer program based on the algorithm ofBrutlag et al. (Comp. App. Biosci. (1990) 6:237-245.) In a sequencealignment the query and subject sequences are both DNA sequences. An RNAsequence can be compared by converting U's to T's. The result of saidglobal sequence alignment is in percent identity. Preferred parametersused in a FASTDB alignment of DNA sequences to calculate percentidentity are: Matrix=Unitary, k-tuple=4, Mismatch Penalty=1, JoiningPenalty=30, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5,Gap Size Penalty 0.05, Window Size=500 or the length of the subjectnucleotide sequence, whichever is shorter.

If the subject sequence is shorter than the query sequence because of 5′or 3′ deletions, not because of internal deletions, a manual correctionmust be made to the results. This is because the FASTDB program does notaccount for 5′ and 3′ truncations of the subject sequence whencalculating percent identity. For subject sequences truncated at the 5′or 3′ ends, relative to the query sequence, the percent identity iscorrected by calculating the number of bases of the query sequence thatare 5′ and 3′ of the subject sequence, which are not matched/aligned, asa percent of the total bases of the query sequence. Whether a nucleotideis matched/aligned is determined by results of the FASTDB sequencealignment. This percentage is then subtracted from the percent identity,calculated by the above FASTDB program using the specified parameters,to arrive at a final percent identity score. This corrected score iswhat is used for the purposes of the present invention. Only basesoutside the 5′ and 3′ bases of the subject sequence, as displayed by theFASTDB alignment, which are not matched/aligned with the query sequence,are calculated for the purposes of manually adjusting the percentidentity score.

For example, a 90 base subject sequence is aligned to a 100 base querysequence to determine percent identity. The deletions occur at the 5′end of the subject sequence and therefore, the FASTDB alignment does notshow a matched/alignment of the first 10 bases at 5′ end. The 10unpaired bases represent 10% of the sequence (number of bases at the 5′and 3′ ends not matched/total number of bases in the query sequence) so10% is subtracted from the percent identity score calculated by theFASTDB program. If the remaining 90 bases were perfectly matched thefinal percent identity would be 90%. In another example, a 90 basesubject sequence is compared with a 100 base query sequence. This timethe deletions are internal deletions so that there are no bases on the5′ or 3′ of the subject sequence which are not matched/aligned with thequery. In this case the percent identity calculated by FASTDB is notmanually corrected. Once again, only bases 5′ and 3′ of the subjectsequence which are not matched/aligned with the query sequence aremanually corrected for. No other manual corrections are to be made forthe purposes of the present invention.

Some embodiments of the invention encompass a nucleic acid moleculecomprising at least 10, 20, 30, 35, 40, 50, 60, 70, 80, 90, 100, 200,300, 400, 500, 600, 700, or 800 consecutive nucleotides or more of anyof SEQ ID NOs:1-20, or domains, fragments, variants, or derivativesthereof.

The polynucleotide of the present invention may be in the form of RNA orin the form of DNA, which DNA includes cDNA, genomic DNA, and syntheticDNA. The DNA may be double stranded or single-stranded, and if singlestranded can be the coding strand or non-coding (anti-sense) strand. Thecoding sequence which encodes the mature polypeptide can be identical tothe coding sequence encoding SEQ ID NO:21-40, 46, or 52-56, or may be adifferent coding sequence which coding sequence, as a result of theredundancy or degeneracy of the genetic code, encodes the same maturepolypeptide as the DNA of any one of SEQ ID NOs:21-40, 46, or 52-56.

In certain embodiments, the present invention provides an isolatedpolynucleotide comprising a nucleic acid fragment which encodes at least10, at least 20, at least 30, at least 40, at least 50, at least 60, atleast 70, at least 80, at least 90, at least 95, or at least 100 or morecontiguous amino acids of SEQ ID NOs: 21-40, 46, or 52-56.

The polynucleotide encoding for the mature polypeptide of SEQ ID NOs:21-40, 46, or 52-56 or may include: only the coding sequence for themature polypeptide; the coding sequence of any domain of the maturepolypeptide; and the coding sequence for the mature polypeptide (ordomain-encoding sequence) together with non coding sequence, such asintrons or non-coding sequence 5′ and/or 3′ of the coding sequence forthe mature polypeptide.

Thus, the term “polynucleotide encoding a polypeptide” encompasses apolynucleotide which includes only sequences encoding for thepolypeptide as well as a polynucleotide which includes additional codingand/or non-coding sequences.

In further aspects of the invention, nucleic acid molecules havingsequences at least about 90%, 95%, 96%, 97%, 98% or 99% identical to thenucleic acid sequences disclosed herein, encode a polypeptide havingcellobiohydrolase (“Cbh”), endoglucanase (“Eg”) or beta-gluconase(“Bgl”) functional activity. By “a polypeptide having Cbh, Eg or Bglfunctional activity” is intended polypeptides exhibiting activitysimilar, but not necessarily identical, to a functional activity of theCbh, Eg or Bgl polypeptides of the present invention, as measured, forexample, in a particular biological assay. For example, a Cbh, Eg or Bglfunctional activity can routinely be measured by determining the abilityof a Cbh, Eg or Bgl polypeptide to hydrolyze cellulose, or by measuringthe level of Cbh, Eg or Bgl activity.

Of course, due to the degeneracy of the genetic code, one of ordinaryskill in the art will immediately recognize that a large portion of thenucleic acid molecules having a sequence at least 90%, 95%, 96%, 97%,98%, or 99% identical to the nucleic acid sequence of any of SEQ ID NOs:1-20, or fragments thereof, will encode polypeptides having Cbh, Eg orBgl functional activity. In fact, since degenerate variants of any ofthese nucleotide sequences all encode the same polypeptide, in manyinstances, this will be clear to the skilled artisan even withoutperforming the above described comparison assay. It will be furtherrecognized in the art that, for such nucleic acid molecules that are notdegenerate variants, a reasonable number will also encode a polypeptidehaving Cbh, Eg or Bgl functional activity.

The polynucleotides of the present invention also comprise nucleic acidsencoding a H. grisea, T. aurantiacus, T. emersonii, T. reesei, C.lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M.darwinensis, N. walkeri, S. fibuligera, C. luckowense R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, R. flavipes or Arabidopsis thalianacellulase, or domain, fragment, variant, or derivative thereof, fused toa polynucleotide encoding a marker sequence which allows for detectionof the polynucleotide of the present invention. In one emobodiment ofthe invention, expression of the marker is independent from expressionof the cellulase. The marker sequence may be a yeast selectable markerselected from the group consisting of URA3, HIS3, LEU2, TRP1, LYS2 orADE2. Casey, G. P. et al., “A convenient dominant selection marker forgene transfer in industrial strains of Saccharomyces yeast: SMR1 encodedresistance to the herbicide sulfometuron methyl,” J. Inst. Brew.94:93-97 (1988).

Codon Optimized Polynucleotides

According to one embodiment of the invention, the polynucleotidesencoding heterologous cellulases can be codon-optimized. As used hereinthe term “codon-optimized coding region” means a nucleic acid codingregion that has been adapted for expression in the cells of a givenorganism by replacing at least one, or more than one, or a significantnumber, of codons with one or more codons that are more frequently usedin the genes of that organism.

In general, highly expressed genes in an organism are biased towardscodons that are recognized by the most abundant tRNA species in thatorganism. One measure of this bias is the “codon adaptation index” or“CAI,” which measures the extent to which the codons used to encode eachamino acid in a particular gene are those which occur most frequently ina reference set of highly expressed genes from an organism.

The CAI of codon optimized sequences of the present inventioncorresponds to between about 0.8 and 1.0, between about 0.8 and 0.9, orabout 1.0. A codon optimized sequence may be further modified forexpression in a particular organism, depending on that organism'sbiological constraints. For example, large runs of “As” or “Ts” (e.g.,runs greater than 4, 4, 5, 6, 7, 8, 9, or 10 consecutive bases) can beremoved from the sequences if these are known to effect transcriptionnegatively. Furthermore, specific restriction enzyme sites may beremoved for molecular cloning purposes. Examples of such restrictionenzyme sites include PacI, AscI, BamHI, BglII, EcoRI and XhoI.Additionally, the DNA sequence can be checked for direct repeats,inverted repeats and mirror repeats with lengths of ten bases or longer,which can be modified manually by replacing codons with “second best”codons, i.e., codons that occur at the second highest frequency withinthe particular organism for which the sequence is being optimized.

Deviations in the nucleotide sequence that comprise the codons encodingthe amino acids of any polypeptide chain allow for variations in thesequence coding for the gene. Since each codon consists of threenucleotides, and the nucleotides comprising DNA are restricted to fourspecific bases, there are 64 possible combinations of nucleotides, 61 ofwhich encode amino acids (the remaining three codons encode signalsending translation). The “genetic code” which shows which codons encodewhich amino acids is reproduced herein as Table 2. As a result, manyamino acids are designated by more than one codon. For example, theamino acids alanine and proline are coded for by four triplets, serineand arginine by six, whereas tryptophan and methionine are coded by justone triplet. This degeneracy allows for DNA base composition to varyover a wide range without altering the amino acid sequence of theproteins encoded by the DNA.

TABLE 2 The Standard Genetic Code T C A G T TTT Phe (F) TCT Ser (S) TATTyr (Y) TGT Cys (C) TTC Phe (F) TCC Ser (S) TAC Tyr (Y) TGC TTA Leu (L)TCA Ser (S) TAA Ter TGA Ter TTG Leu (L) TCG Ser (S) TAG Ter TGG Trp (W)C CTT Leu (L) CCT Pro (P) CAT His (H) CGT Arg (R) CTC Leu (L) CCC Pro(P) CAC His (H) CGC Arg (R) CTA Leu (L) CCA Pro (P) CAA Gln (Q) CGA Arg(R) CTG Leu (L) CCG Pro (P) CAG Gln (Q) CGG Arg (R) A ATT Ile (I) ACTThr (T) AAT Asn (N) AGT Ser (S) ATC Ile (I) ACC Thr (T) AAC Asn (N) AGCSer (S) ATA Ile (I) ACA Thr (T) AAA Lys (K) AGA Arg (R) ATG Met ACG Thr(T) AAG Lys (K) AGG Arg (R) (M) G GTT Val (V) GCT Ala (A) GAT Asp (D)GGT Gly (G) GTC Val (V) GCC Ala (A) GAC Asp (D) GGC Gly (G) GTA Val (V)GCA Ala (A) GAA Glu (E) GGA Gly (G) GTG Val (V) GCG Ala (A) GAG Glu (E)GGG Gly (G)

Many organisms display a bias for use of particular codons to code forinsertion of a particular amino acid in a growing peptide chain. Codonpreference or codon bias, differences in codon usage between organisms,is afforded by degeneracy of the genetic code, and is well documentedamong many organisms. Codon bias often correlates with the efficiency oftranslation of messenger RNA (mRNA), which is in turn believed to bedependent on, inter alia, the properties of the codons being translatedand the availability of particular transfer RNA (tRNA) molecules. Thepredominance of selected tRNAs in a cell is generally a reflection ofthe codons used most frequently in peptide synthesis. Accordingly, genescan be tailored for optimal gene expression in a given organism based oncodon optimization.

Given the large number of gene sequences available for a wide variety ofanimal, plant and microbial species, it is possible to calculate therelative frequencies of codon usage. Codon usage tables are readilyavailable, for example, athttp://phenotype.biosci.umbc.edu/codon/sgd/index.php (visited May 7,2008) or at http://www.kazusa.or.jp/codon/ (visited Mar. 20, 2008), andthese tables can be adapted in a number of ways. See Nakamura, Y., etal. “Codon usage tabulated from the international DNA sequencedatabases: status for the year 2000” Nucl. Acids Res. 28:292 (2000).Codon usage tables for yeast, calculated from GenBank Release 128.0 [15Feb. 2002], are reproduced below as Table 3. This table uses mRNAnomenclature, and so instead of thymine (T) which is found in DNA, thetables use uracil (U) which is found in RNA. The Table has been adaptedso that frequencies are calculated for each amino acid, rather than forall 64 codons.

TABLE 3 Codon Usage Table for Saccharomyces cerevisiae Genes Frequencyper Amino Acid Codon Number hundred Phe UUU 170666 26.1 Phe UUC 12051018.4 Total Leu UUA 170884 26.2 Leu UUG 177573 27.2 Leu CUU 80076 12.3Leu CUC 35545 5.4 Leu CUA 87619 13.4 Leu CUG 68494 10.5 Total Ile AUU196893 30.1 Ile AUC 112176 17.2 Ile AUA 116254 17.8 Total Met AUG 13680520.9 Total Val GUU 144243 22.1 Val GUC 76947 11.8 Val GUA 76927 11.8 ValGUG 70337 10.8 Total Ser UCU 153557 23.5 Ser UCC 92923 14.2 Ser UCA122028 18.7 Ser UCG 55951 8.6 Ser AGU 92466 14.2 Ser AGC 63726 9.8 TotalPro CCU 88263 13.5 Pro CCC 44309 6.8 Pro CCA 119641 18.3 Pro CCG 345975.3 Total Thr ACU 132522 20.3 Thr ACC 83207 12.7 Thr ACA 116084 17.8 ThrACG 52045 8.0 Total Ala GCU 138358 21.2 Ala GCC 82357 12.6 Ala GCA105910 16.2 Ala GCG 40358 6.2 Total Tyr UAU 122728 18.8 Tyr UAC 9659614.8 Total His CAU 89007 13.6 His CAC 50785 7.8 Total Gln CAA 17825127.3 Gln CAG 79121 12.1 Total Asn AAU 233124 35.7 Asn AAC 162199 24.8Total Lys AAA 273618 41.9 Lys AAG 201361 30.8 Total Asp GAU 245641 37.6Asp GAC 132048 20.2 Total Glu GAA 297944 45.6 Glu GAG 125717 19.2 TotalCys UGU 52903 8.1 Cys UGC 31095 4.8 Total Trp UGG 67789 10.4 Total ArgCGU 41791 6.4 Arg CGC 16993 2.6 Arg CGA 19562 3.0 Arg CGG 11351 1.7 ArgAGA 139081 21.3 Arg AGG 60289 9.2 Total Gly GGU 156109 23.9 Gly GGC63903 9.8 Gly GGA 71216 10.9 Gly GGG 39359 6.0 Total Stop UAA 6913 1.1Stop UAG 3312 0.5 Stop UGA 4447 0.7

By utilizing this or similar tables, one of ordinary skill in the artcan apply the frequencies to any given polypeptide sequence, and producea nucleic acid fragment of a codon-optimized coding region which encodesthe polypeptide, but which uses codons optimal for a given species.Codon-optimized coding regions can be designed by various differentmethods.

In one method, a codon usage table is used to find the single mostfrequent codon used for any given amino acid, and that codon is usedeach time that particular amino acid appears in the polypeptidesequence. For example, referring to Table 3 above, for leucine, the mostfrequent codon is UUG, which is used 27.2% of the time. Thus all theleucine residues in a given amino acid sequence would be assigned thecodon UUG.

In another method, the actual frequencies of the codons are distributedrandomly throughout the coding sequence. Thus, using this method foroptimization, if a hypothetical polypeptide sequence had 100 leucineresidues, referring to Table 3 for frequency of usage in the S.cerevisiae, about 5, or 5% of the leucine codons would be CUC, about 11,or 11% of the leucine codons would be CUG, about 12, or 12% of theleucine codons would be CUU, about 13, or 13% of the leucine codonswould be CUA, about 26, or 26% of the leucine codons would be UUA, andabout 27, or 27% of the leucine codons would be UUG.

These frequencies would be distributed randomly throughout the leucinecodons in the coding region encoding the hypothetical polypeptide. Aswill be understood by those of ordinary skill in the art, thedistribution of codons in the sequence can vary significantly using thismethod; however, the sequence always encodes the same polypeptide.

When using the methods above, the term “about” is used precisely toaccount for fractional percentages of codon frequencies for a givenamino acid. As used herein, “about” is defined as one amino acid more orone amino acid less than the value given. The whole number value ofamino acids is rounded up if the fractional frequency of usage is 0.50or greater, and is rounded down if the fractional frequency of use is0.49 or less. Using again the example of the frequency of usage ofleucine in human genes for a hypothetical polypeptide having 62 leucineresidues, the fractional frequency of codon usage would be calculated bymultiplying 62 by the frequencies for the various codons. Thus, 7.28percent of 62 equals 4.51 UUA codons, or “about 5,” i.e., 4, 5, or 6 UUAcodons, 12.66 percent of 62 equals 7.85 UUG codons or “about 8,” i.e.,7, 8, or 9 UUG codons, 12.87 percent of 62 equals 7.98 CUU codons, or“about 8,” i.e., 7, 8, or 9 CUU codons, 19.56 percent of 62 equals 12.13CUC codons or “about 12,” i.e., 11, 12, or 13 CUC codons, 7.00 percentof 62 equals 4.34 CUA codons or “about 4,” i.e., 3, 4, or 5 CUA codons,and 40.62 percent of 62 equals 25.19 CUG codons, or “about 25,” i.e.,24, 25, or 26 CUG codons.

Randomly assigning codons at an optimized frequency to encode a givenpolypeptide sequence, can be done manually by calculating codonfrequencies for each amino acid, and then assigning the codons to thepolypeptide sequence randomly. Additionally, various algorithms andcomputer software programs are readily available to those of ordinaryskill in the art. For example, the “EditSeq” function in the LasergenePackage, available from DNAstar, Inc., Madison, Wis., thebacktranslation function in the VectorNTl Suite, available fromInforMax, Inc., Bethesda, Md., and the “backtranslate” function in theGCG—Wisconsin Package, available from Accelrys, Inc., San Diego, Calif.In addition, various resources are publicly available to codon-optimizecoding region sequences, e.g., the “backtranslation” function athttp://www.entelechon.com/bioinformatics/backtranslation.php?lang=eng(visited Apr. 15, 2008) and the “backtranseq” function available athttp://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html (visited Jul. 9, 2002).Constructing a rudimentary algorithm to assign codons based on a givenfrequency can also easily be accomplished with basic mathematicalfunctions by one of ordinary skill in the art.

A number of options are available for synthesizing codon optimizedcoding regions designed by any of the methods described above, usingstandard and routine molecular biological manipulations well known tothose of ordinary skill in the art. In one approach, a series ofcomplementary oligonucleotide pairs of 80-90 nucleotides each in lengthand spanning the length of the desired sequence is synthesized bystandard methods. These oligonucleotide pairs are synthesized such thatupon annealing, they form double stranded fragments of 80-90 base pairs,containing cohesive ends, e.g., each oligonucleotide in the pair issynthesized to extend 3, 4, 5, 6, 7, 8, 9, 10, or more bases beyond theregion that is complementary to the other oligonucleotide in the pair.The single-stranded ends of each pair of oligonucleotides is designed toanneal with the single-stranded end of another pair of oligonucleotides.The oligonucleotide pairs are allowed to anneal, and approximately fiveto six of these double-stranded fragments are then allowed to annealtogether via the cohesive single stranded ends, and then they ligatedtogether and cloned into a standard bacterial cloning vector, forexample, a TOPO® vector available from Invitrogen Corporation, Carlsbad,Calif. The construct is then sequenced by standard methods. Several ofthese constructs consisting of 5 to 6 fragments of 80 to 90 base pairfragments ligated together, i.e., fragments of about 500 base pairs, areprepared, such that the entire desired sequence is represented in aseries of plasmid constructs. The inserts of these plasmids are then cutwith appropriate restriction enzymes and ligated together to form thefinal construct. The final construct is then cloned into a standardbacterial cloning vector, and sequenced. Additional methods would beimmediately apparent to the skilled artisan. In addition, gene synthesisis readily available commercially.

In certain embodiments, an entire polypeptide sequence, or fragment,variant, or derivative thereof is codon optimized by any of the methodsdescribed herein. Various desired fragments, variants or derivatives aredesigned, and each is then codon-optimized individually. In addition,partially codon-optimized coding regions of the present invention can bedesigned and constructed. For example, the invention includes a nucleicacid fragment of a codon-optimized coding region encoding a polypeptidein which at least about 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%of the codon positions have been codon-optimized for a given species.That is, they contain a codon that is preferentially used in the genesof a desired species, e.g., a yeast species such as Saccharomycescerevisiae or Kluveromyces, in place of a codon that is normally used inthe native nucleic acid sequence.

In additional embodiments, a full-length polypeptide sequence iscodon-optimized for a given species resulting in a codon-optimizedcoding region encoding the entire polypeptide, and then nucleic acidfragments of the codon-optimized coding region, which encode fragments,variants, and derivatives of the polypeptide are made from the originalcodon-optimized coding region. As would be well understood by those ofordinary skill in the art, if codons have been randomly assigned to thefull-length coding region based on their frequency of use in a givenspecies, nucleic acid fragments encoding fragments, variants, andderivatives would not necessarily be fully codon optimized for the givenspecies. However, such sequences are still much closer to the codonusage of the desired species than the native codon usage. The advantageof this approach is that synthesizing codon-optimized nucleic acidfragments encoding each fragment, variant, and derivative of a givenpolypeptide, although routine, would be time consuming and would resultin significant expense.

The codon-optimized coding regions can be, for example, versionsencoding a cellobiohydrolase, endoglucanase or beta-glucosidase from H.grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C.formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N.walkeri, S. fibuligera, C. luckowense R. speratus, Thermobfida fusca,Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui,Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromycesequii, Neocallimastix patricarum, Aspergillus kawachii, Heteroderaschachtii, H. jecorina, Orpinomyces sp., Irpex lacteus, Acremoniumthermophilum, Neosartorya fischeri, Chaetomium globosum, Chaetomiumthermophilum, Aspergillus fumigatus, Aspergillus terreus, NeurosporaCrassa, R. flavipes, or Arabidopsis thaliana, or domains, fragments,variants, or derivatives thereof.

Codon optimization is carried out for a particular species by methodsdescribed herein, for example, in certain embodiments codon-optimizedcoding regions encoding polypeptides of H. grisea, T. aurantiacus, T.emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C.acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C. luckowenseR. speratus, Thermobfida fusca, Clostridum thermocellum, Clostridiumcellulolyticum, Clostridum josui, Bacillus pumilis, Cellulomonas fimi,Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum,Aspergillus kawachii, Heterodera schachtii, H. jecorina, Orpinomycessp., Irpex lacteus, Acremonium thermophilum, Neosartorya fischeri,Chaetomium globosum, Chaetomium thermophilum, Aspergillus fumigatus,Aspergillus terreus, Neurospora Crassa, R. flavipes, or Arabidopsisthaliana cellulases, or domains, fragments, variants, or derivativesthereof are optimized according to yeast codon usage, e.g.,Saccharomyces cerevisiae, Kluyveromyces lactis and/or Kluyveromycesmarxianus. Also provided are polynucleotides, vectors, and otherexpression constructs comprising codon-optimized coding regions encodingpolypeptides of H. grisea, T. aurantiacus, T. emersonii, T. reesei, C.lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M.darwinensis, N. walkeri, S. fibuligera, C. luckowense R. speratus,Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum,Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagusdegradans, Piromyces equii, Neocallimastix patricarum, Aspergilluskawachii, Heterodera schachtii, H. jecorina, Orpinomyces sp., Irpexlacteus, Acremonium thermophilum, Neosartorya fischeri, Chaetomiumglobosum, Chaetomium thermophilum, Aspergillus fumigatus, Aspergillusterreus, Neurospora Crassa, R. flavipes, or Arabidopsis thalianacellulases or domains, fragments, variants, or derivatives thereof, andvarious methods of using such polynucleotides, vectors and otherexpression constructs.

In certain embodiments described herein, a codon-optimized coding regionencoding any of SEQ ID NOs:21-40, 46, or 52-56 or domain, fragment,variant, or derivative thereof, is optimized according to codon usage inyeast (Saccharomyces cerevisiae, Kluyveromyces lactis or Kluyveromycesmarxianus). In some embodiments, the sequences are codon-optimizedspecifically for expression in Saccharomyces cerevisiae. In someembodiments, the sequences are codon-optimized for expression inKluyveromyces. In some embodiments, a sequence is simultaneouslycodon-optimized for optimal expression in both Saccharomyces cerevisiaeand in Kluyveromyces. Alternatively, a codon-optimized coding regionencoding any of SEQ ID NOs: 21-40, 46, or 52-56 may be optimizedaccording to codon usage in any plant, animal, or microbial species.

Vectors and Methods of Using Vectors in Host Cells

The present invention also relates to vectors which includepolynucleotides of the present invention, host cells which aregenetically engineered with vectors of the invention and the productionof polypeptides of the invention by recombinant techniques.

Host cells are genetically engineered (transduced or transformed ortransfected) with the vectors of this invention which may be, forexample, a cloning vector or an expression vector. The vector may be,for example, in the form of a plasmid, a viral particle, a phage, etc.The engineered host cells can be cultured in conventional nutrient mediamodified as appropriate for activating promoters, selectingtransformants or amplifying the genes of the present invention. Theculture conditions, such as temperature, pH and the like, are thosepreviously used with the host cell selected for expression, and will beapparent to the ordinarily skilled artisan.

The polynucleotides of the present invention may be employed forproducing polypeptides by recombinant techniques. Thus, for example, thepolynucleotide may be included in any one of a variety of expressionvectors for expressing a polypeptide. Such vectors include chromosomal,nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40;bacterial plasmids; and yeast plasmids. However, any other vector may beused as long as it is replicable and viable in the host.

The appropriate DNA sequence may be inserted into the vector by avariety of procedures. In general, the DNA sequence is inserted into anappropriate restriction endonuclease site(s) by procedures known in theart. Such procedures and others are deemed to be within the scope ofthose skilled in the art.

The DNA sequence in the expression vector is operatively associated withan appropriate expression control sequence(s) (promoter) to direct mRNAsynthesis. Representative examples of such promoters are as follows:

Gene Organism Systematic name Reason for use/benefits PGK1 S. cerevisiaeYCR012W Strong constitutive promoter ENO1 S. cerevisiae YGR254W Strongconstitutive promoter TDH3 S. cerevisiae YGR192C Strong constitutivepromoter TDH2 S. cerevisiae YJR009C Strong constitutive promoter TDH1 S.cerevisiae YJL052W Strong constitutive promoter ENO2 S. cerevisiaeYHR174W Strong constitutive promoter GPM1 S. cerevisiae YKL152C Strongconstitutive promoter TPI1 S. cerevisiae YDR050C Strong constitutivepromoter

Additionally, promoter sequences from stress and starvation responsegenes are useful in the present invention. In some embodiments, promoterregions from the S. cerevisiae genes GAC1, GET3, GLC7, GSH1, GSH2, HSF1,HSP12, LCB5, LRE1, LSP1, NBP2, PIL1, PIM1, SGT2, SLG1, WHI2, WSC2, WSC3,WSC4, YAP1, YDC1, HSP104, HSP26, ENA1, MSN2, MSN4, SIP2, SIP4, SIP5,DPL1, IRS4, KOG1, PEP4, HAP4, PRB1, TAX4, ZPR1, ATG1, ATG2, ATG10.ATG11, ATG12, ATG13, ATG14, ATG15, ATG16, ATG17, ATG18, and ATG19 may beused. Any suitable promoter to drive gene expression in the host cellsof the invention may be used. Additionally the E. coli, lac or trp, andother promoters known to control expression of genes in prokaryotic orlower eukaryotic cells can be used.

In addition, the expression vectors may contain one or more selectablemarker genes to provide a phenotypic trait for selection of transformedhost cells such as URA3, HIS3, LEU2, TRP1, LYS2 or ADE2, dihydrofolatereductase, neomycin (G418) resistance or zeocin resistance foreukaryotic cell culture, or tetracycline or ampicillin resistance in E.coli.

The expression vector may also contain a ribosome binding site fortranslation initiation and/or a transcription terminator. The vector mayalso include appropriate sequences for amplifying expression, or mayinclude additional regulatory regions.

The vector containing the appropriate DNA sequence as herein, as well asan appropriate promoter or control sequence, may be employed totransform an appropriate host to permit the host to express the protein.

Thus, in certain aspects, the present invention relates to host cellscontaining the above-described constructs. The host cell can be a hostcell as described elsewhere in the application. The host cell can be,for example, a lower eukaryotic cell, such as a yeast cell, e.g.,Saccharomyces cerevisiae or Kluyveromyces, or the host cell can be aprokaryotic cell, such as a bacterial cell.

As representative examples of appropriate hosts, there may be mentioned:bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium;thermophilic or mesophlic bacteria; fungal cells, such as yeast; andplant cells, etc. The selection of an appropriate host is deemed to bewithin the scope of those skilled in the art from the teachings herein.

Appropriate fungal hosts include yeast. In certain aspects of theinvention the yeast is selected from the group consisting ofSaccharomyces cerevisiae, Kluyveromyces lactis, Schizzosaccharomycespombe, Candida albicans, Pichia pastoris, Pichia stipitis, Yarrowialipolytica, Hansenula polymorpha, Phaffia rhodozyma, Candida utilis,Arxula adeninivorans, Debaryomyces hansenii, Debaryomyces polymorphus,Schwanniomyces occidentalis, Issatchenkia orientalis, Kluyveromycesmarxianus, Blakeslea, Candida, Cryptococcus, Cunninghamella, Lipomyces,Mortierella, Mucor, Phycomces, Pythium, Rhodosporidium, Rhodotorula,Trichosporon and Yarrowia.

Methods of Using Host Cells to Produce Ethanol

The present invention is also directed to use of host cells andco-cultures to produce ethanol from cellulosic substrates. Such methodscan be accomplished, for example, by contacting a cellulosic substratewith a host cell or a co-culture of the present invention.

Numerous cellulosic substrates can be used in accordance with thepresent invention. Substrates for cellulose activity assays can bedivided into two categories, soluble and insoluble, based on theirsolubility in water. Soluble substrates include cellodextrins orderivatives, carboxymethyl cellulose (CMC), or hydroxyethyl cellulose(HEC). Insoluble substrates include crystalline cellulose,microcrystalline cellulose (Avicel), amorphous cellulose, such asphosphoric acid swollen cellulose (PASC), dyed or fluorescent cellulose,and pretreated lignocellulosic biomass. These substrates are generallyhighly ordered cellulosic material and thus only sparingly soluble.

It will be appreciated that suitable lignocellulosic material may be anyfeedstock that contains soluble and/or insoluble cellulose, where theinsoluble cellulose may be in a crystalline or non-crystalline form. Invarious embodiments, the lignocellulosic biomass comprises, for example,wood, corn, corn stover, sawdust, bark, leaves, agricultural andforestry residues, grasses such as switchgrass, ruminant digestionproducts, municipal wastes, paper mill effluent, newspaper, cardboard orcombinations thereof.

In some embodiments, the invention is directed to a method forhydrolyzing a cellulosic substrate, for example a cellulosic substrateas described above, by contacting the cellulosic substrate with a hostcell of the invention. In some embodiments, the invention is directed toa method for hydrolyzing a cellulosic substrate, for example acellulosic substrate as described above, by contacting the cellulosicsubstrate with a co-culture comprising yeast cells expressingheterologous cellulases.

In some embodiments, the invention is directed to a method forfermenting cellulose. Such methods can be accomplished, for example, byculturing a host cell or co-culture in a medium that contains insolublecellulose to allow saccharification and fermentation of the cellulose.

The production of ethanol can, according to the present invention, beperformed at temperatures of at least about 30° C., about 31° C., about32° C., about 33° C., about 34° C., about 35° C., about 36° C., about37° C., about 38° C., about 39° C., about 40° C., about 41° C., about42° C., about 43° C., about 44° C., about 45° C., about 46° C., about47° C., about 48° C., about 49° C., or about 50° C. In some embodimentsof the present invention the thermotolerant host cell can produceethanol from cellulose at temperatures above about 30° C., about 31° C.,about 32° C., about 33° C., about 34° C., about 35° C., about 36° C.,about 37° C., about 38° C., about 39° C., about 40° C., about 41° C.,about 42° C., or about 43° C., or about 44° C., or about 45° C., orabout 50° C. In some embodiments of the present invention, thethermotolterant host cell can produce ethanol from cellulose attemperatures from about 30° C. to 60° C., about 30° C. to 55° C., about30° C. to 50° C., about 40° C. to 60° C., about 40° C. to 55° C. orabout 40° C. to 50° C.

In some embodiments, methods of producing ethanol can comprisecontacting a cellulosic substrate with a host cell or co-culture of theinvention and additionally contacting the cellulosic substrate withexternally produced cellulase enzymes. Exemplary externally producedcellulase enzymes are commercially available and are known to those ofskill in the art.

Therefore, the invention is also directed to methods of reducing theamount of externally produced cellulase enzymes required to produce agiven amount of ethanol from cellulose comprising contacting thecellulose with externally produced cellulases and with a host cell orco-culture of the invention. In some embodiments, the same amount ofethanol production can be achieved using at least about 5%, 10%, 15%,20%, 25%, 30%, or 50% less externally produced cellulases. In someembodiments, no external cellulase is added, or less than about 5% ofthe cellulase is externally added cellulase, or less than about 10% ofthe cellulase is externally added cellulase, or less than about 15% ofthe cellulase is externally added cellulase.

In some embodiments, the methods comprise producing ethanol at aparticular rate. For example, in some embodiments, ethanol is producedat a rate of at least about 0.1 mg per hour per liter, at least about0.25 mg per hour per liter, at least about 0.5 mg per hour per liter, atleast about 0.75 mg per hour per liter, at least about 1.0 mg per hourper liter, at least about 2.0 mg per hour per liter, at least about 5.0mg per hour per liter, at least about 10 mg per hour per liter, at leastabout 15 mg per hour per liter, at least about 20.0 mg per hour perliter, at least about 25 mg per hour per liter, at least about 30 mg perhour per liter, at least about 50 mg per hour per liter, at least about100 mg per hour per liter, at least about 200 mg per hour per liter, atleast about 300 mg per hour per liter, at least about 400 mg per hourper liter, or at least about 500 mg per hour per liter.

In some embodiments, the host cells of the present invention can produceethanol at a rate of at least about 0.1 mg per hour per liter, at leastabout 0.25 mg per hour per liter, at least about 0.5 mg per hour perliter, at least about 0.75 mg per hour per liter, at least about 1.0 mgper hour per liter, at least about 2.0 mg per hour per liter, at leastabout 5.0 mg per hour per liter, at least about 10 mg per hour perliter, at least about 15 mg per hour per liter, at least about 20.0 mgper hour per liter, at least about 25 mg per hour per liter, at leastabout 30 mg per hour per liter, at least about 50 mg per hour per liter,at least about 100 mg per hour per liter, at least about 200 mg per hourper liter, at least about 300 mg per hour per liter, at least about 400mg per hour per liter, or at least about 500 mg per hour per liter morethan a control strain (lacking heterologous cellulases) and grown underthe same conditions. In some embodiments, the ethanol can be produced inthe absence of any externally added cellulases.

Ethanol production can be measured using any method known in the art.For example, the quantity of ethanol in fermentation samples can beassessed using HPLC analysis. Many ethanol assay kits are commerciallyavailable that use, for example, alcohol oxidase enzyme based assays.Methods of determining ethanol production are within the scope of thoseskilled in the art from the teachings herein.

The following embodiments of the invention will now be described in moredetail by way of these non-limiting examples.

EXAMPLES

The present invention presents a number of important steps forward forcreating a yeast capable of consolidated bioprocessing. It describesimproved cellulolytic yeast created by expressing combinations ofheterologous cellulases. The present invention demonstrates for thefirst time, the ability of transformed Kluyveromyces to produce ethanolfrom cellulose, the ability of yeast strains expressing only secretedheterologous cellulases to produce ethanol from cellulose, and theability of co-cultures of multiple yeast strains expressing differentcellulases to produce ethanol from cellulose. In addition such yeaststrains and co-cultures of yeast strains can increase the efficiency ofsimultaneous saccharification and fermentation (SSF) processes.

General Protocols

General Strain Cultivation and Media

Escherichia coli strain DH5α (Invitrogen), or NEB 5 alpha (New EnglandBiolabs) was used for plasmid transformation and propagation. Cells weregrown in LB medium (5 g/L yeast extract, 5 g/L NaCl, 10 g/L tryptone)supplemented with ampicillin (100 mg/L), kanamycin (50 mg/L), or zeocin(20 mg/L). When zeocin selection was desired LB was adjusted to pH 7.0.Also, 15 g/L agar was added when solid media was desired.

Yeast strains were routinely grown in YPD (10 g/L yeast extract, 20 g/Lpeptone, 20 g/L glucose), YPC (10 g/L yeast extract, 20 g/L peptone, 20g/L cellobiose), or YNB+glucose (6.7 g/L Yeast Nitrogen Base withoutamino acids, and supplemented with appropriate amino acids for strain,20 g/L glucose) media with either G418 (250 mg/L unless specified) orzeocin (20 mg/L unless specified) for selection. 15 g/L agar was addedfor solid media.

Molecular Methods

Standard protocols were followed for DNA manipulations (Sambrook et al.1989). PCR was performed using Phusion polymerase (New England Biolabs)for cloning, and Taq polymerase (New England Biolabs) for screeningtransformants, and in some cases Advantage Polymerase (Clontech) for PCRof genes for correcting auxotrophies. Manufacturers guidelines werefollowed as supplied. Restriction enzymes were purchased from NewEngland Biolabs and digests were set up according to the suppliedguidelines. Ligations were performed using the Quick ligation kit (NewEngland Biolabs) as specified by the manufacturer. Gel purification wasperformed using either Qiagen or Zymo research kits, PCR product anddigest purifications were performed using Zymo research kits, and Qiagenmidi and miniprep kits were used for purification of plasmid DNA.Sequencing was performed by the Molecular Biology Core Facility atDartmouth College. Yeast mediated ligation (YML) was used to create someconstructs (Ma et al. Gene 58:201-216 (1987)). This was done by creatingDNA fragments to be cloned with 20-40 bp of homology with the otherpieces to be combined and/or the backbone vector. A backbone vector(pRS426), able to replicate in yeast, and with the Ura3 gene forselection, was then transformed into yeast by standard methods with thetarget sequences for cloning. Transformed yeast recombine thesefragments to form a whole construct and the resulting plasmid allowsselection on media without uracil.

Vectors

Plasmid constructs vectors in the experiments detailed below aresummarized in Table 4, and the primers used in vector construction areshown in Table 5.

TABLE 4 Plasmids used. Plasmid Genotype pBKD1-BGLI bla KanMXPGK1_(P)-S.f. bgl1-PGK1_(T) pBKD2-sEGI bla KanMX ENO1_(P)-sT.r.eg1-ENO1_(T) pBKD1-BGLI-sEGI bla KanMX ENO1_(P)-sT.r. eg1-ENO1_(T) &PGK1_(P)-S.f. bgl1-PGK1_(T) YEpENO-BBH bla URA3 ENO1_(PT) pJC1 La grangeet al. bla URA3 PGK_(PT) (1996) pRDH101 bla URA3ENO1_(P)-sT.r.cbh1-ENO1_(T) pRDH103 bla URA3 ENO1_(P)-sH.g.cbh1-ENO1_(T)pRDH104 bla URA3 ENO1_(P)-sT.a.cbh1-ENO1_(T) pRDH105 bla URA3ENO1_(P)-sT.e.cbh1-ENO1_(T) pRDH106 bla URA3 ENO1_(P)-sT.e.cbh2-ENO1_(T)pRDH107 bla URA3 PGK1_(P)-sT.r.cbh2-PGK1_(T) pRDH108 bla URA3PGK1_(P)-sT.r.cbh2-PGK1_(T) & ENO1_(P)-sT.e.cbh1-ENO1_(T) pRDH118 blaURA3 PGK1_(P)-sT.r.cbh2-PGK1_(T) & ENO1_(P)-sH.g.cbh1-ENO1_(T) pRDH120bla URA3 PGK1_(P)-sT.r.cbh2-PGK1_(T) & ENO1_(P)-sT.a.cbh1-ENO1_(T) pDF1La Grange et al. bla fur1::LEU2 (1996) pCEL5 Den Haan et al. 2 micronvector for expression of SfBGLI and 2007 TrEGI (native sequence) pMU185pUG66 (loxp-zeo-loxp) pKLAC1 New England K. lactis expression vector forintegration at Biolabs the lac4 locus, acetamide selection pRS426 2micron vector for yeast mediated ligation (YML) pMU289 pRS426 withportion of pKLAC1 for insertion of TrEG1 (from pBKD_11621, as detailedin example 1) into lac4 locus created by YML pMU291 pRS426 with portionof pKLAC1 for insertion of TrCBH2 (from pBZD_20641, as detailed inexample 1) into lac4 locus created by YML pMU398ENO1_(P)-sT.e.cbh1-ENO1_(T) from pRDH105 into pMU289 (cloning by YML)pMU451 pRDH105 with PacI/AscI linker (formed using primers) insertedinto EcoRI/XhoI pMU458 synthetic construct for N.f. EG inserted intopMU451 (PacI/AscI digest of both pieces) pMU463 TrEG1 frompBKD1-BGLI-sEGI into pMU451 (PacI/AscI digest of both pieces) pMU465synthetic construct for C.l.(a) EG inserted into pMU451 (PacI/AscIdigest of both pieces) pMU469 synthetic construct for R.f.EG insertedinto pMU451 (PacI/AscI digest of both pieces) pMU471 synthetic constructfor C.f.EG inserted into pMU451 (PacI/AscI digest of both pieces) pMU472synthetic construct for N.t.EG inserted into pMU451 (PacI/AscI digest ofboth pieces) pMU473 synthetic construct for C.a.EG inserted into pMU451(PacI/AscI digest of both pieces) pMU475 synthetic construct for T.r.CBH2 derived from pBKD_20641 with tether removed (from example 1)inserted into pMU451 (PacI/AscI digest of both pieces) pMU499 syntheticconstruct for M.d. EG inserted into pMU451 (PacI/AscI digest of bothpieces) pMU500 synthetic construct for R.s. EG inserted into pMU451(PacI/AscI digest of both pieces) pMU503 synthetic construct for N.w. EGinserted into pMU451 (PacI/AscI digest of both pieces) pMU624/pMI529 2micron vector for expression of T.e. CBH1 w/CBD (PCR fragments forchimeric enzyme with PmlI-XhoI digested pRDH105) pMU326 syntheticconstruct for R.s. EG from Codon Devices pMU784/pMI574 2 micron vectorfor expression of C.l.(b) CBH2 (synthetic construct for C.l.(b) CBH2inserted into PacI/AscI digested pMU624) pMU562 pBKD_2 withloxp-zeo-loxp inserted (NotI digest of both pieces) pMU576ENO1p-T.r.cbh1-ENO1_(T) (from pMU291) in pMU562 (PacI/AscI digest ofboth pieces) pMU577 ENO1p-T.e.cbh1-ENO1_(T) in (from pMU398) pMU562(PacI/AscI digest of both pieces) pMU661 ENO1p-T.r. EG1-ENO1_(T) (frompMU463) in pMU562 (PacI/AscI digest of both pieces) pMU662 ENO1p-C.l.(a)EG1-ENO1_(T) (from pMU465) in pMU562 (PacI/AscI digest of both pieces)pMU663 ENO1p-C.f. EG1-ENO1_(T) (from pMU471) in pMU562 (PacI/AscI digestof both pieces) pMU664 ENO1p-N.t. EG1-ENO1_(T) (from pMU472) in pMU562(PacI/AscI digest of both pieces) pMU665 ENO1p-C.a. EG1-ENO1_(T) (frompMU473) in pMU562 (PacI/AscI digest of both pieces) pMU666ENO1p-T.r.CBH2-ENO1_(T) (from pMU475) in pMU562 (PacI/AscI digest ofboth pieces) pMU667 ENO1p-M.d.-EG1-ENO1_(T) (from pMU499) in pMU562(PacI/AscI digest of both pieces) pMU668 ENO1p-N.w.-EG1-ENO1_(T) (frompMU503) in pMU562 (PacI/AscI digest of both pieces) pMU755ENO1p-T.e.CBH1 w/CBD-ENO1_(T) (from pMU624) in pMU562 (PacI/AscI digestof both pieces) pMU750 ENO1p-R.s.-EG2-ENO1_(T) (from pMU326) in pMU562(PacI/AscI digest of both pieces) pMU809 ENO1p-C.l.(b) CBH2b-ENO1_(T)(from pMU784) in pMU562 (PacI/AscI digest of both pieces) pMU721 pMU562with hph gene (hygromycin resistance marker) replacing zeocin marker(NotI digest for both fragments) pMU760 ENO1p-T.e.CBH1 w/CBD-ENO1_(T)from pMU624 in pMU721 (MheI/AscI digest for both fragments) pMU761ENO1p-T.r.CBH2-ENO1_(T) from pMU291in pMU721 (PacI/AscI digest for bothfragments) pMI553 2 micron vector for expression of T.r. CBH2 and T.e.CBH1 + CBM pMI568 2 micron vector for expression of T.r. EG1, please seetext for description of how this construct was built. pMI574 2 micronvector for expression of C.l.(b) CBH2 pMI577 2 micron vector forexpression of T.r. CBH2 and H.g. CBH1 pMI578 2 micron vector forexpression of T.r. CBH2 and T.e. CBH1 pMI579 2 micron vector forexpression of T.r. CBH2 and C.l.(b) CBH1 pMI580 2 micron vector forexpression of C.l.(b) CBH2 and T.e. CBH1 + CBM pMI581 2 micron vectorfor expression of C.l.(b) CBH2 and T.e. CBH1 pMI582 2 micron vector forexpression of C.l.(b) CBH2 and H.g. CBH1 pMI583 2 micron vector forexpression of C.l.(b) CBH2 and C.t. CBH1

-   Abbreviations: ENO1_(P/T)=Enolase 1 gene promoter/terminator;    PGK1_(P/T)=phosphoglycerate kinase 1 gene promoter & terminator;    Tr.=Trichoderma reesei; H.g.=Humicola grisea; T.a.=Thermoascus    aurantiacus; Te.=Talaromyces emersonii, S.f.=Saccharomycopsis    fibuligera; C.l. (a)=Coptotermes lacteus; C.f.=Coptotermes    formosanus; N.t.=Nasutitermes takasagoensis; C.a.=Coptotermes    acinaciformis; M.d.=Mastotermes darwinensis; N.w.=Nasutitermes    walkeri; R.s.=Reticulitermes speratus; C.l. (b)=Chrysosporium    lucknowense; NJ.=Neosartorya fischeri; R.f.=Reticulitermes flavipes;    C.t.=Chaetomium thermophilum

TABLE 5 Primers Used sCBH1/2-L GACTGAATTCATAATGGTCTCCTTCACCTCC (SEQ IDNO: 59) sCBH1-R GACTCTCGAGTTACAAACATTGAGAGTAGTATGG (SEQ ID NO: 60)sCBH2-R CAGTCTCGAGTTACAAGAAAGATGGGTTAGC (SEQ ID NO: 61) 395 Te cbh1Synt1 PacI- GCGTTGGTACCGTTTAAACGGGGCCCTTAATTAAACAAT ATGGCTAAGAAGAGCTTTACTATTGAG (SEQ ID NO: 62) 398 Te cbh1 synt coreCCTCCCCCGGGTTAGAAGCAGTGAAAGTGGAGTTGATTG SmaI G (SEQ ID NO: 63) 399Trcbh1synt CBM5 GCGACGAGTCAACCCTCCAGGTGGTAACAGAGGTACTA MlyIHincII CCAC (SEQ IDNO: 64) 400 Trcbh1 synt CBM GCGACTCGAGGGCGCGCCTACAAACATTGAGAGTAGTAAscIXhoI TGGGTTTA (SEQ ID NO: 65) 379 ScPGK1prom-786GCGTTGAGCTCGGGCCCTAATTTTTATTTTAGATTCCTGA SacI + ApaI CTTCAAC (SEQ ID NO:66) 380 ScPGK1prom EcoRI- GCGTTGAATTCTTAATTAAGTAAAAAGTAGATAATTACT PacITCCTTG (SEQ ID NO: 67) 381 CBH2 WT EcoRI-GCGTTGAATTCTTAATTAAACAATGATTGTCGGCATTCT PacI-ATG CACCACGC (SEQ ID NO:68) 386 CBH2 WT TAA-AscI- gcgatgaattcggcgcgccTTACAGGAACGATGGGTTTGCGTTTGEcoRI (SEQ ID NO: 69)

The yeast expression vector YEpENO-BBH was created to facilitateheterologous expression under control of the S. cerevisiae enolase 1(ENO1) gene promoter and terminator. The vector was also useful becausethe expression cassette from this vector could be simply excised using aBamHI, BglII digest. YEpENO1 (Den Haan et al., Metabolic Engineering. 9:87-942007) contains the YEp352 backbone with the ENO1 gene promoter andterminator sequences cloned into the BamHI and HindIII sites. Thisplasmid was digested with BamHI and the overhang filled in with Klenowpolymerase and dNTPs to remove the BamHI site. The plasmid wasre-ligated to generate YEpENO-B. Using the same method, the BglII andthen the HindIII sites were subsequently destroyed to createYEpENO-BBHtemplate. YEpENO-BBHtemplate was used as template for a PCRreaction with primers ENOBB-left (5′-GATCGGATCCCAATTAATGTGAGTTACCTCA-3′(SEQ ID NO: 70)) and ENOBB-right(5′-GTACAAGCTTAGATCTCCTATGCGGTGTGAAATA-3′ (SEO ID NO: 71)) in which theENO1 cassette was amplified together with a 150 bp flanking regionupstream and 220 bp downstream. This product was digested with BamHI andHindIII and the over hangs filled in by treatment with Klenow polymeraseand dNTPs and cloned between the two PvuII sites on yENO1 effectivelyreplacing the original ENO1 cassette and generating YEpENO-BBH. Codonoptimized versions of Humicola grisea cbh1 (Hgcbh1), Thermoascusaurantiacus cbh1 (Tacbh1) and Talaromyces emersonii cbh1 and cbh2(Tecbh1 and Tecbh2) were designed and synthetic genes were ordered fromGenScript Corporation (Piscataway, N.J., USA). These four synthetic cbhencoding genes received from GenScript Corporation were cloned onto theplasmid pUC57. The resulting vectors were digested with EcoRI and XhoIto excise the cbh genes which were subsequently cloned into an EcoRI andXhoI digested YEpENO-BBH. This created the plasmids pRDH103 (withHgcbh1), pRDH104 (with Tacbh1), pRDH105 (with Tecbh1) and pRDH106 (withTecbh2) with the cbh encoding genes under transcriptional control of theENO1 promoter and terminator. Additionally, pRDH101 was created toexpress the T. reesei CBH1 from pBZD_(—)10631_(—)20641. Takara ExTaqenzyme was used as directed and to amplify the sTrcbh1 frompBZD_(—)10631_(—)20641 using primers sCBH1/2 L and sCBH1R. The fragmentwas then isolated and digested with EcoRI and XhoI. YEpENO-BBH was alsodigested with EcoRI and XhoI and the relevant bands were isolated andligated. A 1494 bp fragment encoding the T. reesei cbh2 gene wasamplified from the plasmid pBZD_(—)10631_(—)20641, with primerssCBH1/2-L and sCBH2 R (5′-CAGTCTCGAGTTACAAGAAAGATGGGTTAGC-3′ (SEO ID NO:61)), digested with EcoRI and XhoI and cloned into the EcoRI and XhoIsites of pJC1 (Crouse et al., Curr. Gen. 28: 467-473 (1995)) placing itunder transcriptional control of S. cerevisiae phosphoglycerate kinase 1(PGK1) gene promoter and terminator. This plasmid was designatedpRDH107. Subsequently the expression cassettes from pRDH103, pRDH104 andpRDH105 were excised with BamHI and BglII digestion and cloned into theBamHI site of pRDH107 to yield pRDH118, pRDH120, pRDH108 and pRDH109,respectively. pRDH109 contains the same expression cassettes as pRDH108but in pRDH108 the gene expression cassettes are in the reverseorientation relative to each other. These plasmids and their basicgenotypes are summarized in Table 4.

Two additional 2-micron vectors for expression of Chrysosporiumlucknowense CBH2b and the T. emersonii CBH1 with a c-terminal fusion ofthe CBM of T. reesei CBH1 were also created. The fusion between T.emersonii cbh1 and the CBM of T. reesei cbh1 was generated by ligationof three fragments. Table 5 lists the oligonucleotides used for theseconstructs. A PCR product was amplified with the oligonucleotides 395 Tecbh1 Syntl PacI-ATG and 398 Te cbh1 synt core SmaI using pRDH105 as thetemplate, digested with PmlI and SmaI and the 800 bp fragment wasisolated. A second PCR product was amplified with oligonucleotides 399Trcbh1 synt CBM5 MlyIHincII and 400 Trcbh1 synt CBM AscIXhol withpRDH101 as the template, digested with MlyI and XhoI and the 180 bpfragment was isolated. The two PCR fragments were ligated with the 6.9kb PmlI-XhoI fragment of pRDH105 resulting in pMU624.

The genomic 3900 bp DNA sequence of Chrysosporium lucknowense cbh2b gene(described in Published United States Patent Application No:2007/0238155) was analyzed for putative introns using the NetAspGene 1.0Server (http://www.cbs.dtu.dk/services/NetAspGene/). Removal of thepredicted introns from the genomic sequence resulted in an open readingframe of 482 amino acids which was synthesized at Codon Devices andcodon optimized for expression in S. cerevisiae and cloned into pUC57vector. Plasmid pAJ401 (Saloheimo et al. Mol. Microbiol. 13:219-228,1994), which contains the PGK1 promoter and terminator, was modified forexpression of T. reesei cbh2 between Pad and AscI restrictions sites.The PGK1 promoter was amplified with primers 379 ScPGK1prom −786SacI+ApaI and 380 ScPGK1prom EcoRI-PacI and pAJ410 as the template anddigested with Pad and EcoRI. The T. reesei cbh2 ORF was amplified frompTTc01 (Teen et al., Gene 51:43-52, 1987) with oligonucleotides 381 CBH2WT EcoRI-PacI-ATG and 386 CBH2 WT TAA-AscI-EcoRI, digested with Pad andEcoRI, and ligated with the SacI-EcoRI digested pAJ401 resulting inpMI508. The PacI-AscI fragment in pMI508 was replaced by a synthetic 1.4kb T. reesei egll gene resulting in pMI522. The 1.9 kb fragment ofpMI522 was digested with PmlI and XhoI and ligated to the 6.4 kbPmlI-XhoI fragment of pRDH107 resulting in pMI568. pMI568 was digestedwith Pad and AscI and the 7 kb fragment was ligated to the 1.5 kbfragment of pMI558 producing pMU784 for the expression of C. lucknowensecbh2b.

A set of 2-micron vectors was also constructed for the expression ofendoglucanases in S. cerevisiae, as well as related plasmids to act ascontrols. pMU451 was created as a control vector and for cloning thecellulases under control of the ENO1 promoter and terminator. This wasdone by adding a PacI/AscI linker into the EcoRI/XhoI site of pMU451.Synthetic genes ordered from Codon Devices and received in pUC57 werecloned into this vector as PacI/AscI fragments. Vectors created this wayand listed in Table 4 are: pMU458, pMU463, pMU465, pMU469, pMU471,pMU472, pMU473, pMU475, pMU499, pMU500, and pMU503.

Vectors for integrating secreted versions of cellulases at the deltaintegration sites in S. cerevisiae, or for integration into the genomeof K. marxianus were created from the pBKD_(—)1 and pBKD_(—)2constructs. The S. fibuligera BGL1 (SfBGLI) was cloned by PCR from ySFI(van Rooyen et al., J. Biotechnol. 120: 284-95 (2005)). Theendoglucanase (TrEGI) used was the sequence give in Table 1. Thecellulase encoding genes were cloned via PCR (using Pad and AscI sites)into pBKD_(—)1 and pBKD_(—)2—to create pBKD1-BGL1 and pBKD2-sEG1. TheENO1P-sEG1-ENO1T cassette from pBKD2-sEG1 was subsequently sub cloned asa SpeI, NotI fragment to pBKD1-BGL1 to create pBKD1-BGL1-sEG1.

pMU562, used for integrating cellulases into K. marxianus, was generatedby cutting with pMU185 (pUG66) with Not1 and isolating a 1190 bp lox PZeoR containing insert. This insert was ligated into a Not1 digested 4.5Kb delta-integration vector to produce pMU562. pMU576 was generated bycutting T. reesei CBH2 containing plasmid pMU291 with Asc1/Pac1,isolating a 1491 bp CBH2 gene and ligating it into delta-integrationvector pMU562 cut with Asc1/Pac1. pMU577 was generated by cutting T.emersonii CBH1 from pMU398 with Asc1/Pac1, isolating a 1380 bp CBH1 geneand ligating into delta-integration vector pMU562 cut with Asc1/Pac1.Similarly, a set of recombinant cellulase constructs (pMU661 to pMU668and pMU750, pMU755, pMU809—see Table 4), including a variety ofendoglucanases and cellobiohydrolases, was incorporated into pMU562 forco-transformation. Synthetic sequences for these cellulase genes wereoriginally obtained from Codon Devices and subsequently cloned into 2μexpression vectors for use in S. cerevisiae. They were then transferredfrom these vectors to the integrating vectors as detailed (includingdigests used) in Table X. Together these constructs formed a librarythat could be transformed separately or together and then screened byactivity assay. Constructs were digested with enzymes that cut insideof, or very closely outside of, the delta sequences for integration.Similar constructs for integrating cellulases using the hygromycinmarker (pMU721, pMU760, and pMU761) were also built.

Yeast Transformation

For routine transformation of whole plasimds in S. cerevisiae, standardchemical transformation was used (Sambrook et al. Molecular cloning: Alaboratory manual. New York: Cold Spring Harbor Laboratory Press(1989)). For some transformations, a modified protocol described by Hillet al. (Nucleic Acids Res. 19: 5791 (1991)) was used.

A protocol for electrotransformation of yeast was developed based on Choet al. (1999) and on Ausubel et al. (1994). Linear fragments of DNA werecreated by digesting pBD1-BGL1-sEG1 with AccI. AccI has a unique site inthe δ sequence. The fragments were purified by precipitation with 3MNaAc and ice cold ethanol, subsequent washing with 70% ethanol, andresuspension in USB dH2O (DNAse and RNAse free, sterile water) afterdrying in a 70° C. vacuum oven.

S. cerevisiae cells for transformation were prepared by growing tosaturation in 5 mL YPD cultures. 4 mL of the culture was sampled, washed2× with cold distilled water, and resuspended in 640 μL cold distilledwater. 80 μL of 100 mM Tris-HCl, 10 mM EDTA, pH 7.5 (10×TE buffer—filtersterilized) and 80 μL of 1 M lithium acetate, pH 7.5 (10×LiAc—filtersterilized) were added, and the cell suspension was incubated at 30° C.for 45 mM with gentle shaking. 20 μL of 1M DTT was added and incubationcontinued for 15 min. The cells were then centrifuged, washed once withcold distilled water, and once with electroporation buffer (1M sorbitol,20 mM HEPES), and finally resuspended in 267 μL electroporation buffer.The same protocol was used for transforming K. lactis and K. marxianusstrains, except that 50 mLs of YPD was inoculated with 0.5 mL from anovernight culture, grown for 4 hours at 37° C., and then centrifuged andprepared as above. Additionally, incubations and recovery steps werecarried out at 37° C.

For electroporation, 10 μg of linearized DNA (measured by estimation ona gel) was combined with 50 μL of the cell suspension in a sterile 1.5mL microcentrifuge tube. The mixture was then transferred to a 0.2 cmelectroporation cuvette, and a pulse of 1.4 kV (200μ, 25 μF) was appliedto the sample using the Biorad Gene Pulser device. 1 mL of YPD with 1Msorbitol adjusted to pH 7.0 (YPDS) was placed in the cuvette and thecells were allowed to recover for ˜3 hrs. 100-200 μL cell suspensionwere spread out on YPDS agar plates with appropriate antibiotic, whichwere incubated at 30° C. for 3-4 days until colonies appeared.

Yeast Strains

The yeast strains listed in Table 6 were created using the vectors andtransformation protocols as described.

TABLE 6 Yeast Strains. Background Genes expressed and/or Name strainknocked out Constructs M0013 Saccharomyces Genotype: α, leu2-3,112ura3-52 None cerevisiae his3 trp1-289 Y294 (ATCC 201160) M0243 M0013SfBGLI, TrEGI pBKD1-BGLI-sEGI M0244 M0013 SfBGLI, TrEGI (nativesequence) pCEL5 M0247 M0013 TeCBH1; delta FUR1 pRDH105 M0248 M0013TrCBH2, TeCBH1; delta FUR1 pRDH108; pDF1 M0249 M0013 None (control);delta FUR1 pJC1; pDF1 M0265 M0013 HgCBHI; delta FUR1 pRDH103; pDF1 M0266M0013 TaCBHI; delta FUR1 pRDH104; pDF1 M0282 M0248 SfBGLI, TrEGI,TrCBH2, pBKD1-BGLI-sEGI; TeCBH1; delta FUR1 pRDH108; pDF1 M0284 M0243SfBGLI, TrEGI, TrCBH2, pBKD1-BGLI-sEGI; HgCBH1; delta FUR1 pRDH118; pDF1M0286 M0243 SfBGLI, TrEGI, TrCBH2, pBKD1-BGLI-sEGI; TaCBH1; delta FUR1pRDH120; pDF1 M0288 M0243 SfBGLI, TrEGI, TrCBH2, pBKD1-BGLI-sEGI;TeCBH1; delta FUR1 pRDH108; pDF1 M0289 M0013 TrCBH2, HgCBH1; delta FUR1pRDH118; pDF1 M0291 M0013 TrCBH2, TaCBH1; delta FUR1 pRDH120; pDF1 M0358M0282 SfBGLI, TrEGI, TrCBH2, pBKD1-BGLI-sEGI; TeCBH1; delta FUR1; Trp1;His3 pRDH108; pDF1 M0359 M0288 SfBGLI, TrEGI, TrCBH2, pBKD1-BGLI-sEGI;TeCBH1; delta FUR1; Trp1; His3 pRDH108; pDF1 M0361 M0249 None (control);delta FUR1; pJC1; pDF1 Trp1; His3 M0157 Kluyveromyces None Nonemarxianus (ATCC #10606) M0158 Kluyveromyces None None lactis (ATCC#34440) M0411 M0158 (colony SfBGLI, TrEGI pBKD1-BGLI-sEGI; #1) M0412M0158 (colony SfBGLI, TrEGI pBKD1-BGLI-sEGI; #2) M0413 M0157 (ColonySfBGLI, TrEGI pBKD1-BGLI-sEGI; #1) M0414 M0157 (Colony SfBGLI, TrEGIpBKD1-BGLI-sEGI; #2) M0491 M0414 SfBGLI, TrEGI, TeCBH1, pBKD1-BGLI-sEGI;TrCBH2 pMU576 and pMU577 M0599 M0414 SfBGLI, TrEGI, TeCBH1,pBKD1-BGLI-sEGI; TrCBH2 pMU760 and pMU761 M0600 M0414 SfBGLI, TrEGI,TeCBH1, pBKD1-BGLI-sEGI; TrCBH2 pMU760 and pMU761 M0601 to M0414 (11SfBGLI, TrEGI, pBKD1-BGLI-sEGI; M0604; colonies Cl(a)EG, CfEG, NtEG,CaEG, pMU663, pMU755, M0611 to displaying MdEG, NwEG, RsEG, TeCBH1,pMU809, pMU576, M0617 highest TeCBH1 + CBD, TrCBH2, pMU661, pMU662,avicelase Cl(b)CBH2 pMU664, pMU665, activity) pMU667, pMU668, pMU750,pMU577 M0618 to M0157(8 Cl(a)EG, CfEG, NtEG, CaEG, pMU663, pMU755, M0625colonies MdEG, NwEG, RsEG, TeCBH1, pMU809, pMU576, displaying TeCBH1 +CBD, TrCBH2, pMU661, pMU662, highest Cl(b)CBH2 pMU664, pMU665, avicelasepMU667, pMU668, activity) pMU750, pMU577 yENO1 M0013 ENO1 P/TYEpENO-BBH; pDF1 M0419 M0013 ENO1 P/T pMU451 M0420 M0013 TeCBH1 pMU272M0423 M0013 TrEG1 pMU463 M0424 M0013 SfBGL1 pMU464 M0426 M0013 RfEGpMU469 M0446 M0013 Cl(a)EG pMU465 M0449 M0013 CfEG pMU471 M0450 M0013NtEG pMU472 M0460 M0013 MdEG pMU499 M0461 M0013 RsEG pMU500 M0464 M0013NwEG pMU503 M0476 M0013 NfEG pMU458 Y294/pMI529 M0013 TeCBH1 + CBMpMU624 fur1Δ Y294/pMI553 M0013 TrCBH2, TeCBH1 + CBM pMI553 fur1ΔY294/pMI574 M0013 Cl(b)CBH2 pMI574 fur1Δ Y294/pMI577 M0013 TrCBH2,HgCBH1 pMI577 fur1Δ Y294/pMI578 M0013 TrCBH2, TeCBH1 pMI578 fur1ΔY294/pMI579 M0013 TrCBH2, Cl(b)CBH1 pMI579 fur1Δ Y294/pMI580 M0013Cl(b)CBH2, TeCBH1 + CBM pMI580 fur1Δ Y294/pMI581 M0013 Cl(b)CBH2, TeCBH1pMI581 fur1Δ Y294/pMI582 M0013 Cl(b)CBH2, HgCBH1 pMI582 fur1ΔY294/pMI583 M0013 Cl(b)CBH2, Cl(b)CBH1 pMI583 fur1Δ

The plasmid pBKD1-BGL1-sEG1 (pMU276) was digested with AccI andtransformed to S. cerevisiae Y294 bp electrotransformation to create astrain with delta integrated copies of the SfBGLI and TrEGI, designatedMO243. Episomal plasmids were then transformed to S. cerevisiae Y294and/or MO243.

To create autoselective S. cerevisiae strains, i.e. strains that can begrown in medium without requiring selective pressure to maintain theepisomal plasmid, strains were transformed with NsiI & NcoI digestedpDF1 and selected on SC-ura-leu plates. This lead to the disruption ofthe FUR1 gene of S. cerevisiae. PCR was used to confirm FUR1 disruptionwith primers FUR1-left (5′-ATTTCTTCTTGAACCATGAAC-3′ (SEQ ID NO: 72)) andFUR1-right (5′-CTTAATCAAGACTTCTGTAGCC-3′ (SEQ ID NO: 73)), where a 2568bp indicated a disruption.

MO282 was created by transforming MO248 with AccI digestedpBKD1-BGLI-sEGI, as described above, except that the transformationmixture was spread on plated containing 10 g/L BMCC with 10 g/L yeastextract and 20 g/L peptone.

The presence of integrated genes was verified by colony PCR forKluyveromyces strains. Selected yeast strains were made prototrophic bytransforming with PCR products for genes to complement theirauxotrophies.

Cellulosic Substrates for Enzyme Assays

Bacterial microcrystalline cellulose (BMCC) was a gift from CP Kelcocompany. BMCC as received was stirred O/N at 4 C in water. After thesubstrate was rehydrated, it was washed 6 times with water andresuspended in water. The dry weight of the substrate was measured bydrying samples at 105 C until constant weight was obtained.

Avicel PH105 (FMC Biopolymers) was used as provided by the manufacturer.

Pretreated mixed hardwoods were generated by autohydrolysis of thesubstrate at 160 PSI for 10 minutes. Pretreated material was washed 5times to remove inhibitors and soluble sugars and resuspended indistilled water. Samples were dried overnight at 105 C to determine thedry weight. Analysis of sugar content by quantitative saccharificationshowed a 50% glucan content.

Phosphoric acid swollen cellulose (PASC) was prepared as in Zhang andLynd (2006), with only slight modifications. Avicel PH105 (10 g) waswetted with 100 mL of distilled water in a 4 L flask. 800 mL of 86.2%phosphoric acid was added slowly to the flask with a first addition of300 mL followed by mixing and subsequent additions of 50 mL aliquots.The transparent solution was kept at 4° C. for 1 hour to allow completesolubilization of the cellulose, until no lumps remained in the reactionmixture. Next, 2 L of ice-cooled distilled water was added in 500 mLaliquots with mixing between additions. 300 mL aliquots of the mixturewere centrifuged at 5,000 rpm for 20 minutes at 2° C. and thesupernatant removed. Addition of 300 mL cold distilled water andsubsequent centrifugation was repeated 4×. 4.2 mL of 2M sodium carbonateand 300 mL of water were added to the cellulose, followed by 2 or 3washes with distilled water, until the final pH was ˜6. Samples weredried to constant weight in a 105° C. oven to measure the dry weight.

Enzyme Assays

β-glucosidase activity was measured in a manner similar to McBride, J.E., et al., (Enzyme Microb. Techol. 37: 93-101 (2005)), except that thevolume of the assay was decreased and the reaction performed in amicrotiter plate. Briefly, yeast strains were grown to saturation in YPDor YPC media with or without appropriate antibiotics, the opticaldensity at 600 nm (OD(600)) was measured, and an 0.5 mL sample of thecultures was taken. This sample was centrifuged, the supernatant wasseparated and saved, and the cell pellet was washed 2×50 mM citratebuffer, pH 5.0. Reactions for supernatants were made up of 50 μL sample,50 μL citrate buffer, and 50 μL 20 mM p-nitrophenyl-13-D-glucopyranoside(PNPG) substrate. Reactions with washed cells consisted of 25 μL ofcells, 75 μL citrate buffer, and 50 μL PNPG substrate. If the activitywas too high for the range of the standard curve, a lower cellconcentration was used and the assay was re-run. The standard curveconsisted of a 2-fold dilution series of nitrophenol (PNP) standards,starting at 500 nM, and ending at 7.8 nM, and a buffer blank wasincluded. After appropriate dilutions of supernatant or cells wereprepared, the microtiter plate was incubated at 37° C. for 10 minutesalong with the reaction substrate. The reaction was carried out byadding the substrate, incubating for 30 min., and stopping with 150 μLof 2M Na₂CO₃. The plate was then centrifuged at 2500 rpm for 5 minutes,and 150 μL of supernatant was transferred to another plate. Theabsorbance at 405 nm was read for each well.

Endoglucanase activity was qualitatively detected by observing clearingzones on synthetic complete media (as above, but including 20 g/Lglucose) plates with 0.1% carboxymethyl cellulose (CMC) stained withcongo red (Beguin, Anal. Biochem. 131: 333-6 (1983)). Cells were grownfor 2-3 days on the plates and were washed off the plate with 1MTris-HCL buffer pH 7.5. The plates were then stained for 10 minutes witha 0.1% Congo red solution, and extra dye was subsequently washed offwith 1M NaCl.

CBH1 activity was detected using the substrate4-Methylumbelliferyl-β-D-lactoside (MULac). Assays were carried out bymixing 50 μL of yeast supernatant with 50 μL of a 4 mM MUlac substratesolution made in 50 mM citrate buffer pH 5.5. The reaction was allowedto proceed for 30 minutes and then stopped with 1M Na₂CO₃. Thefluorescence in each well was read in a microtiter plate reader (ex. 355nm and em. 460 nm).

Quantification of Enzyme Activity

Enzyme activity on PASC and Avicel were measured using the protocoldescribed in Den Haan et al., Enzyme and Microbial Technology 40:1291-1299 (2007). Briefly, yeast supernatants were incubated withcellulose at 4° C. to bind the cellulase. The cellulose was thenfiltered from the yeast supernatant, resuspended in citrate buffer andsodium azide, and incubated at 37° C. Accumulation of sugar was measuredin the reaction by sampling and performing a phenol-sulfuric acid assay.(See Example 10 and Table 9.)

Avicel activity levels were also generated using a 96-well plate method.(See Example 2.) Strains to be tested were grown in YPD in deep-well 96well plates at 35° C. with shaking at 900 RPM. After growing, plateswere centrifuged at 4000 rpm for 10 min. 300 μL substrate (2% avicel, 50mM sodium acetate buffer, 0.02% sodium azide, β-glucosidase—1 μL per mL)was added to a new 96-well deep well plate, without allowing the avicelto settle. 300 μL of yeast supernatant was added to this substrate, and100 μL was taken for an initial sample. The assay plate is incubated at35° C., with shaking at 800 rpm, and samples were taken at 24 and 48hours. Samples were placed in 96-well PCR plates, and spun at 2000 rpmfor 2 minutes. 50 μL of supernatant was then added to 100 μL of DNSreagent previously placed in a separate 96 well PCR plate, mixed, andheated to 99° C. for 5 minutes in a PCR machine, followed by cooling to4° C. 50 μL was transferred to a microtiter plate and the absorbance wasmeasured at 565 nm. The conversion of avicel was calculated as follows:

$Y = {{\left( {{{OD}\left( {T = {24\mspace{14mu} {or}\mspace{14mu} 48}} \right)} - {{OD}\left( {T = 0} \right)}} \right) \times 100\%} = {\frac{\Delta \; {OD} \times 100}{S \times A} = \frac{\Delta \; {OD} \times 100}{0.1 \times 10}}}$

Y—% of Avicel converted at 24 or 48 hrsS—DNS/glucose calibration slope that is 0.1 for DNS at 565 nmA—Avicel concentration at T=0 that is 10 g/L for 1% Avicel

Example 1 Production of Kluyveromyces Expressing Heterologousβ-Glucosidase and Endoglucanase

In order to test the ability of Kluyveromyces to express functionalheterologous cellulases, two Kluyveromyces strains, Kluyveromycesmarxianus (ATCC strain #10606; MO157) and Kluyveromyces lactis (ATCCstrain #34440), were transformed with vectors encoding heterolgouscellulases.

Vectors containing yeast delta integration sequences, the KanMX markerand sequences encoding S.f. BGLI and Tr. EGI (pBKD-BFLI-sEG1) weretransformed into Kluyveromyces according to the yeast transformationprotocol as described above, and selected on G418. Transformants wereverified by PCR and then tested by CMC assay. The results are shown inFIG. 1. The presence of the heterologous cellulase activity is indicatedby a clearing zone on the CMC plate. As shown in FIG. 1, neither anuntransformed K. lactis strain (colony 8) or an untransformed K.marxianus strain (colony 16) showed endoglucanase activity. However, 6of 7 transformed K. lactis colonies showed CMCase activity, and all 7transformed K. marxianus colonies showed CMCase activity. MO413 andMO414 were identified as two K. marxianus colonies showing CMCaseactivity.

Example 2 Production of Kluyveromyces expressing CBH1 and CBH2

The ability of Kluyveromyces to express functional heterologouscellobiohydrolases was also examined. In these experiments, K. marxianus(MO157) was transformed with constructs containing T. reesei CBH2, T.emersonii CBH1 or both. Similarly, MO414 (K. marxianus transformed withS.f. BGLI and Tr. EGI) was transformed with constructs containing T.reesei CBH2, T. emersonii CBH1 or both.

Transformations were performed as described in above. CBH1 activity wasthen detected using the substrate 4-Methylumbelliferyl-β-D-lactoside(MU-Lac) as described above. The assay was performed on eight coloniesof each transformant and the three colonies showing the highest activitywere averaged. The results are shown in FIG. 2 and demonstrate thatstrains transformed with T. emersonii CBH1 had high MU-lac activity.

The activity of Kluveromyces strains expressing heterologouscellobiohydrolases on Avicel was also assessed. In one experiment, MO413was transformed with vectors containing T. reesei CBH2 and T. emersoniiCBH1 coding sequences along with a zeocin marker. Novel strain MO491 wascreated by this transformation and showed MU-lactoside activity. In asecond experiment, MO413 was transformed with vectors containing T.reesei CBH2 and T. emersonii CBH1 coding sequences along with ahygromycin marker, and strains MO599 and MO600 were isolated from thistransformation. Activity on Avicel was assessed at 48 hours as describedabove, and the results, shown in FIG. 3, demonstrate that Kluveryomcesexpressing heterologous cellulases have Avicelase activity at 35° C.Avicelase activity at 45° C. was also demonstrated (data not shown).

Example 3 Production of Kluyveromyces Expressing a Library of Cellulases

Kluveromyces strains were also created by transforming yeast with alibrary of cellulases (creation of library was described above). Forexample, MO413 was transformed with a library of cellulases containing azeocin marker to produce novel strains MO601-MO604 and MO611-MO617. Inaddition, MO157 (K. marxianus) was transformed with the same library andnovel strains MO618-M0625 were identified. Activity on Avicel wasassessed at 48 hours as described above, and the results, shown in FIG.3, demonstrate that Kluveryomces transformed with a library ofheterologous cellulases also have Avicelase activity at 35° C.Tranformants of MO157 with the library showed the highest activity.Avicelase activity at 45° C. was also demonstrated (data not shown).

Example 4 Ethanol Production by Transformed Kluyveromyces

In order to determine if Kluyveromyces expressing heterologouscellulases could produce ethanol from Avicel, precultures were grown infor 24 hours in YPD (YPD as above, with 20 g/L glucose; 25 mL in a 250mL shake flask) with shaking at 300 rpm at 35° C. After 24 and 48 hours,40 g/L of additional glucose was added. At 72 hours, the pH of thecultures was adjusted to ˜5.0 with citrate buffer (initial pH of bufferwas 5.5, final concentration was 50 mM), and the culture was added to asealed plastic shake flask containing 5.5 grams of Avicel (finalconcentration 10% (w/v). Avicel PH105 (FMC Biopolymers) was used asprovided by the manufacturer. The culture was incubated at 35° C. withshaking at 150 rpm.

Quantification of ethanol in fermentation samples was carried out byHPLC analysis, and initial ethanol concentrations in bottles (fromprecultures) was subtracted from all subsequent data points (initialethanol concentrations ranged between 0 and about 6 g/L). The initialglucose concentation for all strains except MO603 was 0.000 g/L. Forthis strain it was 0.069 g/L, which would result in a maximum in 0.035g/L of ethanol from the initial sugar.

The results, as shown in FIG. 4, demonstrate that Engineered K.marxianus strains were also able to produce ethanol directly fromAvicel. Strain MO157, the untransformed control, showed a steadydecrease in ethanol concentration over the course of the experiment.This is due to ethanol consumption by the strain because of the presenceof a small amount of oxygen in the flasks.

Of the two strains transformed with T. reesei CBH2 and T. emersonii CBH1with the hygromycin marker (MO599 and M600), one (MO599) showed ethanolproduction. In addition, of the five strains transformed with T. reeseiCBH2 and T. emersonii CBH1 with the zeocin marker, four (MO601, MO602,MO604 and MO491) showed ethanol production. This demonstrates thatengineered thermotolerant K. marxianus are capable of producing ethanoldirectly from the recalcitrant crystalline cellulose, Avicel.

Example 5 Production of S. cerevisiae Expressing Heterologous Cellulases

S. cerevisiae expressing heterologous cellulases were also produced andtested for their ability to grow on media containing bacterialmicrocrystalline cellulose (BMCC). In these experiments, microaerobicconditions were maintained by growing strains on BMCC in sealed hungatetubes with an air atomosphere.

Strains expressing T. emersonii CBH1 and T. reesei CBH2 (MO248) weretransformed with a construct allowing T. reesei EGI and S. fibuligeraBGLI expression (pKD-BGLI-sEGI). That transformation was plated on aBMCC solid agar plate and five colonies appeared on the plate afterseven days (data not shown). Yeast from the largest of the five colonieswas isolated as strain MO282. (MO282 is described in more detail above.)The three control strains were tested for growth on the same plates. Onestrain expressed with T. emersonii CBHI and T. reesei CBH2, and twostrains expressed T. reesei EGI and S. fibuligera BGLI. No coloniesappeared on plates with control yeast strains (data not shown).

The ability of MO282 to grow on BMCC was also tested using liquid media.FIG. 5 shows that MO282, which expresses all 4 secreted cellulases grewto a much greater extent on BMCC than a plasmid only control (MO249), astrain expressing only T. emersonii CBH1 and T. reesei CBH2 (MO249), anda strain expressing 4 tethered cellulases (MO144).

These results indicate that yeast expressing secreted T. emersonii CBH1,T. reesei CBH2, T. reesei EGI and S. fibuligera BGLI heterologously areable to grow on bacterial microcrystalline cellulose.

Example 6 S. cerevisiae Expressing Heterologous Cellulases can ProduceEthanol from Avicel and Pretreated Hardwood

In order to determine if transformed S. cerevisiae can produce ethanoldirectly from cellulose without exogenously added cellulase enzymes,transformed strains were grown on Avicel as the sole carbon source.Avicel PH105 (FMC Biopolymers) was used as provided by the manufacturer.

Avicel media was made using the non-glucose components of syntheticcomplete medium for yeast including, yeast nitrogen base without aminoacids-6.7 g/L, and supplemented with a complete amino acid mix (completesupplemental mixture). In some cases yeast extract (10 g/L) and peptone(20 g/L) (YP) were used as supplements in growth experiments.Cultivation conditions were anaerobic and were maintained by flushingsealed glass bottles with N2 after carbon source addition and beforeautoclaving. Non-carbon media components were added as 10× solutions byfilter sterilizing after autoclaving. Inoculation into Avicel cultureswas done at 20% by volume. Quantification of ethanol in fermentationsamples was carried out by HPLC analysis, and initial ethanolconcentrations in bottles (from precultures) was subtracted from allsubsequent data points.

As shown in FIG. 6, Strain MO288 (expressing S. fibuligera BGLI, T.reesei EGI, T. reesei CBH2, and T. emersonii CBH1) was able to produceethanol directly from avicel PH105 as compared to the control strain(MO249) when YNB media components were used.

The ability of MO288 to produce ethanol from cellulose was alsodemonstrated using pretreated hardwoods. Pretreated mixed hardwoods weregenerated by autohydrolysis of the substrate at 160 PSI for 10 minutes.Pretreated material was washed 5 times to remove inhibitors and solublesugars and resuspended in distilled water. Samples were dried overnightat 105° C. to determine the dry weight. Analysis of sugar content byquantitative saccharification showed a 50% glucan content. Media andculture conditions were as described above for Avicel experiments exceptthat cultures were inoculated at 10% by volume.

The data presented in FIG. 7 demonstrates that MO288 was also able tomake ethanol from pretreated hardwoods without added enzyme. The strainmade ˜0.5 g/L more than the control when YP was used as media, and ˜0.2g/L when YNB was used.

These data demonstrate that yeast expressing secreted T. emersonii CBH1,T. reesei CBH2, T. reesei EGI and S. fibuligera BGLI heterologously areable to produce ethanol from cellulose without the addition of anyexogenous cellulases.

Example 7 Transformed Yeast Strains and Externally Added Cellulases ActSynergistically to Produce Ethanol from Pretreated Mixed Hardwoods

Production of ethanol from biomass is currently achieved using an SSFtype of process where cellulase enzymes are added exogenously to areaction containing pretreated cellulosic biomass, yeast growth media,and yeast. In order to determine if yeast expressing recombinantcellulases could improve this process, recombinant yeast expressingsecreted cellulases were cultured in the presence of a range ofexogenously added cellulase concentrations. Growth and media conditionswere as described in previous examples.

In these experiments, a recombinant yeast strain expressing foursecreted cellulases (MO288) was compared directly to the control strain(MO249) under the same conditions. External cellulases were added atconcentrations of 25 mg cellulase per gram cellulose (100%), 22.5 mgcellulase per gram cellulose (90%), 18.75 mg cellulase per gramcellulose (75%) or 6.25 mg cellulase per gram cellulose (25%).Experiments were also performed without adding any external cellulases(0%). Pretreated mixed hardwoods (prepared as described in examplesabove) at an initial solids concentration of 5% were used as a cellulosesource. The data is presented in FIG. 8. From this data, it is clearthat the strain producing cellulases makes additional ethanol relativeto the control strain for each of the cellulase loading concentrationstested.

In order to examine this effect in more detail, ethanol production atdifferent external cellulase concentrations was evaluated in twodifferent types of media using pretreated mixed hardwood. The resultsare shown in FIG. 9. In YP media, MO288 makes 6-9% more ethanol at thehigher cellulase loadings, only 1% more at a 25% loading, and 100% morewhen no cellulase is loaded. In YNB media MO288 makes 20-40% moreethanol at low cellulase loadings, and ˜10% more ethanol at highercellulase loadings. These results can be used to determine the amount ofcellulase that can be removed from the process with the same overallethanol yield being achieved. For YP media cellulase loading can bereduced ˜15% compared to the control, and for YNB media, cellulaseloading can be reduced ˜5%. At non-zero cellulase loadings ethanolproductivity was increased between 5 and 20% for strains expressingcellulases in YP media as compared to the control. It was increasedbetween 10 and 20% for strains cultured in YNB media compared to thecontrol.

These data demonstrate that previous SSF processes can be improved interms of ethanol yield from biomass and ethanol productivity if strainsexpressing secreted cellulases are used in combination with exogenouslyadded cellulases. Similarly, cellulase loadings required to achieve aparticular percentage of theoretical ethanol yield can be reduced whenstrains expressing recombinant cellulases are added.

Example 8 Transformed Yeast Strains Also Increase Efficiency ofExternally Added Cellulases in the Production of Ethanol from Avicel

To test whether this same trend would hold at high substrateconcentrations these experiments were repeated using 15% Avicel PH105 assubstrate instead of 5% pretreated mixed hardwood. The results are shownin FIGS. 10 and 11. The strain making cellulases (MO288) routinelyproduced more ethanol from Avicel than the control yeast strain (MO249)under identical conditions, even at increased ethanol concentrations(FIG. 10). For example, when 25 mg cellulase per gram cellulose wasloaded in the SSF reaction, the test strain (MO288) produced 54 g/L,while the control (MO249) produced 50 g/L.

To examine cellulase displacement the percentage of theoretical ethanolyield achieved at different cellulase loadings was determined. Theresults presented in FIG. 12 were repeated in triplicate for MO288 andMO249, allowing standard deviations for the increased ethanol yields tobe calculated. The data that can be used for calculating cellulasedisplacement is presented in FIG. 12. FIG. 12 presents cellulase enzymesavings based on theoretical ethanol yield at 168 hours in an SSFexperiment. SSF was performed in 30 ml of nitrogen purged YP+15% Avicelin pressure bottles. External cellulase mix at a ratio of 5 Spyzme:1Novozyme-188 was used. The experiment was continued for 168 hours andsampling was done each day for ethanol estimation by HPLC. The arrows inthe figure depict the necessary cellulase loading needed to achieve thesame ethanol production from cellulose as the control. This loading isconsistently lower than for the control (i.e. the ethanol yield isconsistently higher). For data at 168 hours, the average cellulasedisplacement (amount less that needs to be loaded) is 13.3%±4.9%.

Example 9 Use of Artificial Cbh1 to Produce Ethanol

In order to design a CBH1 protein with efficient cellulase activity, 17CBH1 protein sequences from NCBI database (Table 7) were aligned.

TABLE 7 Fungal CBH1 genes used for alignment. Organism Genbank#Neosartorya fischeri XM_001258277 Gibberella zeae AY196784 Penicilliumjanthinellum X59054 Nectria haematococca AY502070 Fusarium poae AY706934Chaetomium thermophilum AY861347 Aspergillus terreus XM_001214180Penicillium chrysogenum AY790330 Neurospora crassa X77778 Trichodermaviride AY368686 Humicola grisea X17258 Thermoascus aurantiacus AF421954Talaromyces emersonii AAL89553 Trichoderma reesei P62694 PhanerochaeteZ29653 chrysosporium Aspergillus niger XM_001391971 Aspergillus nigerXM_001389539

The artificial protein sequence was designed as a consensus (the mostcommon) sequence for these proteins. The predicted signal sequence wasexchanged by S. cerevisiae alpha mating factor pre signal sequence, andthe sequence of the consensus CBH1 protein is shown below. Capitalletters indicate the S. cerevisiae alpha mating factor pre signalsequence.

(SEQ ID NO: 43) MRFPSIFTAVLFAASSALAqqagtltaethpsltwqkctsggscttvngsvvidanwrwvhatsgstncytgntwdttlcpddvtcaqncaldgadysstygvttsgnslrlnfvtqgsqknvgsrlylmeddttyqmfkllgqeftfdvdvsnlpcglngalyfvamdadggmskypgnkagakygtgycdsqcprdlkfingqanvegwepssndanagignhgsccaemdiweansistaftphpcdtigqtmcegdscggtyssdryggtcdpdgcdfnpyrmgnktfygpgktvdttkkvtvvtqfitgssgtlseikrfyvqngkvipnsestisgvsgnsittdfctaqktafgdtddfakkgglegmgkalaqgmvlvmslwddhaanmlwldstyptdatsstpgaargscdtssgvpadveanspnsyvtfsnikfgpig stftg.

An S. cerevisiae and K. lactis codon optimized sequence for expressingthe CBH1 consensus sequence (SEQ ID NO:44) was developed and is shownbelow.

(SEQ ID NO: 44) atgagatttccttcaatcttcactgctgttttgttcgcagcctcaagtgctttagcacaacaggccggaacattgacagcagaaactcatccttccttaacctggcaaaagtgcacttctggaggttcatgcactacagtgaatggatctgtcgtgatcgatgcaaactggagatgggttcacgcaacttcaggttctaccaactgttataccggaaacacttgggacaccacattgtgcccagatgacgtcacgtgcgctcagaactgtgctttggatggagctgattacagttcaacctatggtgtaactacatccggaaactctttgagattaaacttcgttactcaaggaagtcaaaagaacgttggttctagattgtacttaatggaggacgatacaacctatcaaatgttcaaattgttaggtcaggagttcacctttgacgtagatgtcagtaacttgccatgtgggttaaacggagctttatactttgtggcaatggatgctgacggtggaatgtccaagtatccaggaaacaaagccggtgcaaagtacggtacaggatattgtgattcacagtgccctagagatttgaagttcattaacggtcaagcaaatgtggagggttgggaaccatctagtaacgatgccaatgcgggtattggtaatcatgggtcctgttgcgctgagatggatatctgggaggccaactcaatatctactgcctttacccctcacccatgcgatacaattggtcaaactatgtgcgagggtgattcatgtggtggaacctactcctctgatagatacggaggtacatgcgatccagatggttgcgactttaatccatacagaatgggaaacaaaaccttttacggtcctggaaagacagttgatactaccaagaaagtaacagtcgtgacccagtttatcaccggtagttctggaaccttatccgaaatcaaaagattctacgttcagaacggtaaagtaattccaaacagtgaatctacaatttcaggagtgagtggtaattctattactaccgacttttgtacagctcagaaaacagcatttggtgacaccgatgactttgctaagaagggtggattagaaggtatgggtaaagctttggcccagggaatggtgttagttatgtctttatgggatgatcacgccgcaaatatgttatggttggattcaacatatccaactgatgccacaagtagtacacctggagctgccagaggttcttgtgatacatcttccggtgttccagccgatgtagaagcaaattctcctaactcctatgttaccttctccaatataaagtttggtccaatcggt tcaacattcactggttaa

The codon optimized sequence was inserted into the episomal yeastexpression vector (pMU451) under control of ENO1 promoter and terminatorinto PacI/AscI sites. The resulting expression constructs (pMU505) wastransformed into M0375 host strain that derived from Y294 (M0013) inwhich His3 and Trp1 auxotrophies were rescued by transformation with S.cerevisiae His3 and Trp1 PCR products. The resulting strain expressingthe CBH1 consensus sequence was named MO429.

In order to determine if MO429 had cellulase activity, an Avicelconversion assay was performed as described above and measured at 24hours. As shown in FIG. 14, S. cerevisiae expressing the consensus Cbh1sequence (MO429) showed cellulase activity as compared to a negativecontrol transformed with an empty vector (MO419). The cellulase activityof MO429 was also compared to that of yeast strains expressing otherheterologous cellulases. The strains tested are summarized in Table 8below.

TABLE 8 Cellulytic Strains Used in Avicel Conversion Assay Strain #Description Cellulase Family Organism Activity Signal M0419 MO375 + pMnone none U451 M0420 MO375 + pM CBH1 Fungi Talaromyces exo native U272emersonii M0429 MO375 + pM fungal Fungi N/A exo S.c.αMFpre U505 CBH1consensus M0445 MO375 + pM CBH1 Fungi Neosartorya exo S.c.αMFpre U459fischeri M0456 MO375 + pM CBH1 Fungi Chaetomium exo S.c.αMFpre U495thermophilum M0457 MO375 + pM CBH1 Fungi Aspergillus exo S.c.αMFpre U496terreus M0458 MO375 + pM CBH1 Fungi Penicillium exo S.c.αMFpre U497chrysogenum

All of the strains in Table 8 were derived from the same parental M0375strain and were transformed with an episomal yeast vector. MO420, MO429,MO445, MO456, MO457 and MO458 were created using episomal yeast vectorscontaining the heterologous cellulase genes as listed in the table whichwere codon optimized for expression in S. cerevisiae and K. lactis. Thecellulases in MO429, MO445, MO456, MO457 and MO458 were expressed undercontrol of S. cerevisiae ENO1 promoter and terminator. T. emersonii CBH1was expressed with its own native signal sequence. As shown in FIG. 14,the secreted activity on Avicel of the consensus CBH1 was comparablewith activity of other fungal CBH1s expressed in the same vector and inthe same host strain.

Example 10 Comparison of Cellulase Activity in S. cerevisiae

S. cerevisiae were transformed with polynucleotides encoding a number ofdifferent heterologous cellobiohydrolases and their activity on PASC andAvicel was assessed as described above. The results are shown in thetable below:

TABLE 9 Cellobiohydrolase activity in S. cerevisiae. Act. (PASC) Act.(Avicel) Plasmid Expression Cassette(s) (mU/gDCW) (mU/gDCW) yENO1ENO1p/t  2.68 ± 1.1  2.99 ± 0.7 M0265 ENO1p/t-sH.g.cbh1 32.82 ± 6.534.85 ± 2.0 M0266 ENO1p/t-sT.a.cbh1 38.56 ± 5.9 38.15 ± 4.1 M0247ENO1p/t-sT.e.cbh1  75.60 ± 13.1 21.42 ± 6.1 M0248 PGK1p/t-sT.r.cbh2 &174.35 ± 6.5   40.5 ± 4.9 ENO1p/t-sT.e.cbh1 M0289 PGK1p/t-sT.r.cbh2 &Not measured 106.2 ± 6.8 ENO1p/t-sH.g.cbh1 M0291 PGK1p/t-sT.r.cbh2 & Notmeasured  32.7 ± 5.7 ENO1p/t-sT.a.cbh1

In addition, activity on Avicel was assayed using a 96-plate assay, andthe results are shown in FIG. 14. In the Figure, for each strain, thefirst bar indicates the sugar released at 24 hours, and the second barindicates the sugar released by 48 hours. CBH1s expressed individually,or in combination with T. reesei CBH2 showed some avicelactivity—reaching 10% conversion of avicel in 48 hours. Combinations ofCBH1 with CBH2 from C. lucknowense reached much higher avicelconversions of about 22% conversion in 48 hours in combination with T.emersonii CBH1 with CBD attached.

The avicel activity data for endoglucanases tested in S. cerevisiae isshown in FIG. 15. The data demonstrate that among the EGs tested the C.formosanus EG demonstrated the highest avicel activity when expressed inS. cerevisiae.

Example 11 Co-Cultures of Yeast Strains Expressing DifferentHeterologous Cellulases Produce Ethanol from Avicel

A co-culture of a number of cellulase producing yeast strains alsoshowed the ability to make ethanol from Avicel PH105 in YNB media (FIG.16). In this experiment 5 strains independently producing T. emersoniiCBH1 (MO247), T. aurantiacus CBH1 (MO266), H. grisea CBH1 (MO265), acombination of T. emersonii CBH1 and T. reesei CBH2 (MO248), and acombination of T. reesei EGI and S. fibuligera BGLI (MO244) were mixedin equal proportion by volume and then inoculated at 20% by volume. Eachof the heterologously expressed cellulases in each of these strains wassecreted. Media and culture conditions were as described above forAvicel experiments. The data in FIG. 16 demonstrate that heterologouscellulases do not need to be expressed in an individual yeast strain inorder to produce ethanol from cellulose. Instead, yeast strainsexpressing different secreted heterologous cellulases can be culturedtogether in order to produce ethanol from cellulose without the additionof any exogenous cellulases.

A co-culture using a different combination of cellulases was alsoevaluated. In this set of co-culture experiments, four yeast strainswere cultured together: M0566 (MO424 with FUR deletion): SecretedSfBGLI; M0592 (MO449 with FUR deletion): Secreted CfEGI; M0563 (same asY294/pMI574 furlA): Secreted C1 CBH2b; and M0567 (same as Y294/pMI529furlA): Secreted TeCBH1+CBD. These strains were grown in liquid YPD for3 days, until the culture was saturate for pre-culture. At this pointthey were used to inoculate experiments where avicel (10%) was used asthe substrate, and the 4 strains were mixed at equal volume prior toinoculation.

FIG. 17 demonstrates that the co-cultured strains are capable ofproducing ethanol directly from avicel in the absence of any addedcellulase enzyme. The co-culture produces about 4-fold more ethanolafter 168 hours as compared to the control strain, and about 3-fold morethan MO288.

This co-culture was also used in SSF experiments where Zoomerasecellulase enzyme cocktail was used at 5 different loadings (10 mgprotein/g avicel, 7.5 mg/g, 5 mg/g, and 2.5 mg/g, and 0 mg/g), andstrains were inoculated at 10% by volume.

FIG. 18 presents the raw data for ethanol production at a variety ofcellulase loadings by the co-culture, MO288, and MO249. FIG. 18A showsthat at all cellulase loadings tested, the co-cultured strains producedsignificantly more ethanol than a control not producing cellulase. FIG.18B shows that at all cellulase loadings tested, the co-culture producedmore ethanol than the previously tested strain MO288. FIG. 19 shows thepercentage of the theoretical yield of ethanol that could be achievedwith each of these cultures after 168 hours of SSF using a variety ofcellulase loadings. The data demonstrate that the co-cultured strainswould achieve about a 2-fold reduction in cellulase relative to thecontrol strain, and approximately a 35% reduction compared to MO288.

These data demonstrate that the combination of cellulases in thisco-culture is highly efficient in the production of ethanol.

Example 12 Construction of a Robust Xylose-Utilizing Strain

M0509 (ATCC deposit designation, deposited on Nov. 23, 2009) is a strainof Saccharomyces cerevisiae that combines the ability to metabolizexylose with the robustness required to ferment sugars in the presence ofpretreated hardwood inhibitors. M0509 was created in a three-stepprocess. First, industrial strains of S. cerevisiae were benchmarked toidentify strains possessing a level of robustness/hardiness sufficientfor simultaneous saccharification and fermentation (SSF) of pretreatedmixed hardwood substrates. Strain M0086, a diploid strain of strain ofS. cerevisiae, satisfied this first requirement. Second, M0086 wasgenetically engineered with the ability to utilize xylose, resulting instrain M0407. Third, M0407 was adapted for several weeks in a chemostatcontaining xylose media with pretreatment inhibitors, generating strainM0509.

Strain M0407 was genetically engineered from M0086 to utilize xylose.This engineering required seven genetic modifications. The primarymodification was the functional expression of the heterologous xyloseisomerase gene, XylA, isolated from the anaerobic fungus Piromyces sp.E2. The S. cerevisiae structural genes coding for all five enzymesinvolved in the conversion of xylulose to glycolytic intermediates werealso overexpressed: xylulokinase, ribulose 5-phosphate isomerase,ribulose 5-phosphate epimerase, transketolase and transaldolase. Inaddition, the GRE3 gene encoding aldose reductase was deleted tominimise xylitol production. The seven modified genes are listed in FIG.39. The genetic modifications at the GRE3, RKI1, RPE1, TAL1, and TKL1loci were designed to leave behind minimal vector DNA and no antibioticmarkers. Each locus' DNA was sequenced to confirm the expected results.Each of the seven genetic modifications were sequentially introducedinto strain M0086. FIG. 40 shows the progression of modifications fromtop to bottom together with the designations for the strain at each stepin the process, starting with M0086 and finishing with M0407.

The deletion of GRE3 and the increased expression of RKI1, RPE1, TAL1,and TKL1 involve modifications of the endogenous S. cerevisiae loci. Inthe case of GRE3, both alleles were deleted. For the other four loci,only a single allele was modified. All of the modifications ofendogenous loci required the use of selectable antibiotic markersincluding kan^(r) from the Escherichia coli transposon Tn903 (confersresistance to G418), natl from Streptomyces noursei (confers resistanceto clonNAT/nourseothricin), and dsdA from Escherichia coli (confersresistance to D-serine.) After selection for a desired genomicmodification, the antibiotic marker was excised from the genome usingthe loxP/cre recombinase system. The cre recombinase was carried onplasmid pMU210 which contains a zeocin resistance marker. Loss of pMU210as well as all antibiotic markers was tested on the appropriateselective media. Subsequent PCR genotyping and DNA sequencing confirmedremoval of the antibiotic markers from the modified genomic loci.

The overexpression of RKI1, RPE1, TAL1, and TKL1 was achieved by placingthe S. cerevisiae triose phosphate isomerase promoter, TPI, immediately5′ of each of the four ORFs. For TAL1 and RKI1, small portions of theirendogenous promoters were deleted. To avoid disruption of adjacent ORFsand possible transcriptional regulatory elements, the introduction ofthe TPI promoter at the RPE1 and TKL1 loci was done such that the RPE1and TKL1 loci were duplicated with the duplicate copies of both locibeing regulated by the TPI promoter.

In order to boost M0407's xylose-utilization and increase itspretreatment inhibitor tolerance, the strain was maintained in achemostat for four weeks under the following sequential conditionsdescribed in Table 10.

TABLE 10 Conditions to Improve M0407. Duration Residence (days) Time (h)Media 5 24 YPX, 20 g/L xylose 5 18 YPX, 20 g/L xylose 7 24 YPX + 25% ofa 30% MS129 washate (21.5 g/L xylose) 14 24 YPX + 75% of a 30% MS129washate (~22% solids equivalent)

An aliquot of the adapted chemostat culture was plated on YPXi50% andnine M0407 “adapted” colonies were screened in YPDXi media (100 g/Lglucose, 50 g/L xylose, 25% MS149 pressate). M0407 and MO228 (axylose-utilizing strain created at Mascoma containing XlyA and XKS1 onplasmids) were included as controls. At 24 hours, the glucose had beenentirely consumed by all strains. M0407 and MO228 had utilized 30 and 25g/L of xylose respectively. All nine M0407 “adapted” colonies hadutilized more than 44 g/L of xylose. The highest amount of xyloseconsumed was 48 g/L. This strain was designated M0509.

18S rDNA sequencing was used to confirm strain M0509 as Saccharomycescerevisiae (Kurtzman C P and Robnett, C J; FEMS Yeast Research 3 (2003)417-432). A 1774 bp fragment spanning the 18S rDNA was amplified fromM0509 genomic DNA and sent for sequencing. The 1753 bp of M0509 18S rDNAsequence exhibited a 100% match to the NCBI sequence for S. cerevisiae18S (nucleotide accession #Z75578).

Since strain M0509 was obtained by cultivating M0407 in a chemostat forfour weeks, the length of cultivation separating the two strainsprovides a means to asses the stability of the engineered geneticmodifications. Comparison of the DNA sequence of M0407 and M0509 at theGRE3, RKI1, RPE1, TAL1, and TKL1 loci showed no changes. This suggeststhat the genetic modifications at these loci are genetically stable, atleast under the growth conditions used.

Real Time PCR analysis was used to estimate the copy number ofintegrations of the XylA/XKS1 vector. M0407 has approximately 10 copiesof the vector, whereas M0509 has approximately 20 copies. This suggeststhat the copy number of the XylA/XKS1 vector can be increased byextended cultivation on xylose media.

To further asses the stability of the XylA/XKS1 integrations, M0509 wascultivated for ˜50 generations in liquid media with either glucose orxylose as the sole carbon source. After 50 generations, an individualcolony was isolated from each culture and the number of XylA/XKS1integrations quantified and compared to the original M0509 freezerstock. The colony isolated from the xylose-culture had ˜20 copies ofXylA/XKS1, the same as the freezer stock. The glucose-cultured colonyexhibited a slightly decreased copy number, ˜16.

The slight decrease in XylA/XKS1 copy number of the glucose-colonyraises the question of the strain's performance. To partially addressthis question, xylose consumption was compared between thexylose-isolate, glucose-isolate, and freezer stock. The freezer andxylose-propagated isolates utilized all of the xylose in 24 hours andproduced identical amounts of ethanol, but the glucose-propagated strainconsumed only half as much xylose. FIG. 20.

Example 13 Selection of a Thermotolerant, Robust, Xylose-UtilizingStrain

M1105 is capable of fermentation at temperatures above 40° C. in thepresence of 8 g/L acetate. M1105 was constructed in a M0509 backgroundand is therefore an industrially robust strain capable of convertingboth glucose and xylose into ethanol.

M1105 was isolated following four rounds of selection/adaptation in acytostat as outlined in FIG. 41 and described as follows. Thetemperature was increased from 38° C. to 41° C. during the course of theexperiment. M1017 (ATCC deposit designation ______, deposited on Nov.23, 2009) was isolated from this first cytostat run and was laterconfirmed by PCR of the GRE3 locus to be a descendant of M0509. M1017was used to inoculate a second cytostat run using YMX media (yeastnitrogen base, 2 g/L xylose) at 41° C. M1046 was isolated from thissecond cytostat run. At 42° C. on YPX50, M1046 grew slowly yet with adoubling time 36% shorter than M1017. M1080 was isolated from a cytostatinoculated with M1046 and YMX media at 40° C. M1080 grew with a specificgrowth rate of 0.22 h⁻¹ on YMX at 40° C. M1105 was isolated from M1080based on selection in the cytostat using YPD2X10+acetate media (2 g/Lglucose, 10 g/L xylose, 8 g/L acetate, pH 5.4) at 39° C.

M1105 grows 10-20% faster than M0509 in rich media at 35° C. Inaddition, M1105 has increased acetate tolerance as the strain can growmore quickly than its ancestral strains in the presence of acetate. FIG.21. While the parental strains required glucose for tolerance to acetateat high temperatures, M1105 does not require glucose or complex mediumcomponents to grow in the presence of 7 g/L acetate at pH 5.4.

To test fermentation performance, M1105 was inoculated at approximately0.7 g/L DCW in 18% MS419 using 3.8 mg Zoomerase/g feedstock at 40° C.M1105 produced 3.55% (w/v) ethanol by 168 hours. The time course ispresented in FIG. 22 along with a similar run performed with M1088(described below) for comparison. A similar run using only 0.15 g/L DCWfor inoculum resulted in 2.9% (w/v) ethanol and some sugar accumulationduring the experiment. FIG. 23.

Example 14 Adaptation of a Thermotolerant, Robust, Xylose-UtilizingStrain

M1254 is capable of fermentation at temperatures above 40° C. in thepresence of 12 g/L acetate, exhibiting an increased robustness relativeto the thermotolerant strain M1105.

M1254 was isolated following three rounds of selection/adaptation in acytostat as outlined in Table 11 and FIG. 42 and described as follows.The first cytostat run was inoculated with M1105. YMX media (yeastnitrogen base w/o amino acids, 20 g/L xylose) plus 8 g/L acetate wasused at pH 5.5 and 40° C. M1155 was isolated from this first cytostatrun and used to inoculate a second cytostat containing YPD media (yeastextract, peptone, 20 g/L glucose) plus 12 g/L acetate at pH 5.4 and 41°C. M1202 was isolated from this second cytostat run. M1254 was isolatedfrom a third cytostat run inoculated with both M1155 and M1202 in yeastnitrogen base w/o amino acids+5% solids equivalent MS419 hydrolysatemedia at pH 4.8, 39° C.

TABLE 11 Evolutionary Conditions to Generate M1254 from M1105. ParentalNew Strain(s) Evolutionary Condition Strain M1105 Xylose minimal + 8 g/Lacetate, pH 5.5, 40° C. M1155 M1155 Complex glucose + 12 g/L acetate, pH5.4, 41° C. M1202 M1155 + 5% solids equivalent MS419 hydrolysate + M1254M1202 yeast nitrogen base w/o amino acids, pH 4.8, 39° C.

M1254 grows 7.3±0.9% faster than M1202 and 17±2.0% faster than M1155 in5% solids equivalent MS419 hydrolysate, which is the condition underwhich strain M1254 was selected. However, standard fermentation mediumlimits fermentation performance. Accordingly, use of this strain shouldbe with lower ammonium concentrations, such as 1.1 g/L diammoniumphosphate (DAP) or lower than 3 g/L DAP. FIG. 24 demonstrates the higherfermentation rate using the lower DAP concentration. The fermentationswere performed using 18% MS149, 4 mg external cellulase/g TS, 40° C.,0.5 g/L inoculation DCW M1254 and pH 5.4. The pH was controlled using 5M potassium hydroxide, and 1 g/L magnesium carbonate was fed with eachsolids feeding. All enzyme was front loaded, while the solids were fedat five time points (0, 3, 6, 24, and 48 hours) in equal size feedingsof 3.6% TS.

MO1360 was created from M1254 using the evolutionary conditionsdescribed in Table 12 below.

TABLE 12 Conditions to Generate M1360 from M1254. Parental New Strain(s)Evolutionary Condition Strain M1254 Complex with low xylose + 8 g/Lacetate, pH 5.4, M1339 40° C. M1339 Complex xylose + synthetic inhibitormixture M1360 (including 8 g/L acetate), pH 5.4, 40° C.

M1360, while still substantially inhibited by the synthetic inhibitormixture, grows at 40° C. with a doubling time of approximately 5 hours.FIG. 25. In industrially relevant medium, M1360 is able to generate over60 g/L ethanol from glucose along with 5 g/L dry cell weight in 48 h at40° C. beginning with only 60 mg/L dry cell weight. FIG. 26.

Enzyme activity is known to increase as temperature increases, and thusit is desirable to have thermotolerant S. cerevisiae strains. FIG. 27shows three equivalent SSFs with 18% PHW solids loaded. The reactionscarried out at 40° C. show approximately 17% more ethanol produced thanthe control reaction carried out at 35° C., when both reactions werecarried out at the same external enzyme loading (4 mg/g). This increasedperformance represents a substantial cost savings for the process.

Example 15 Expression of Cellulases in a Robust Xylose-Utilizing Strain

M1088 is capable of secreting three distinct cellulolytic enzymes:β-glucosidase from S. fibuligera (SfBGL), cellobiohydrolase 2b from C.lucknowense (ClCBH2b), and cellobiohydrolase I from T. emersonii fusedto the T. reesei cellobiohydrolase I cellulose binding domain(TeCBH1+CBDTrCBH1). The M1088 genome also contains genes that encode forpolypeptides capable of providing resistance to the followingantibiotics: kanamycin, nourseothricin, and hygromycin B. PlasmidpMU624, which is also present in M1088, contains a gene encoding for apolypeptide capable of providing resistance to ampicillin. The stepsused to generate M1088 and M0963 from M0509 are summarized in Table 13below.

TABLE 13 Strains Used to Generate Strains M1088 and M0963 StrainGenotype Parent Description M0509 gre3::loxP/gre3::loxP TAL1+/loxP-PTPI-TAL1 RKI1+/loxP-PTPI-RKI1 RPE1+/loxP-PTPI-RPE1 TKL+/loxP-PTPI-TKLdelta::PTPI- xylA PADH1-XKS::delta M0539 URA-3/ura-3::kanMX M0509 Asingle copy of the genomic URA-3 gre3::loxP/gre3::loxP TAL1+/loxP- genewas deleted and replaced with a PTPI-TAL1 RKI1+/loxP-PTPI-RKI1 kanMXcassette. The KanMX gene RPE1+/loxP-PTPI-RPE1 cassette providesresistance to TKL+/loxP-PTPI-TKL delta::PTPI- kanamycin (anaminoglycoside xylA PADH1-XKS::delta antibiotic). M0544ura-3::kanMX/ura-3::kanMX M0539 The second copy of the genomicgre3::loxP/gre3::loxP TAL1+/loxP- URA-3 gene was deleted and PTPI-TAL1RKI1+/loxP-PTPI-RKI1 replaced with a kanMX cassette.RPE1+/loxP-PTPI-RPE1 TKL+/loxP-PTPI-TKL delta::PTPI- xylAPADH1-XKS::delta M0749 ura-3::kanMX/ura-3::kanMX M0544 A single copy ofthe genomic FUR-1 gre3::loxP/gre3::loxP TAL1+/loxP- gene was deleted andreplaced with a PTPI-TAL1 RKI1+/loxP-PTPI-RKI1 Streptomyces noursei nat1cassette. RPE1+/loxP-PTPI-RPE1 The nat1 gene cassette providesTKL+/loxP-PTPI-TKL delta::PTPI- resistance to the antibiotic xylAPADH1-XKS::delta nourseothricin/clonNAT (an (pMU782)fur1::nataminoglycoside antibiotic). M0867 FUR-1/fur-1::nat ura-3::kanMX/ura-M0749 The plasmid pMU624 was 3::kanMX gre3::loxP/gre3::loxP transformedinto the strain. pMU624 TAL1+/loxP-PTPI-TAL1 can replicate in S.cerevisiae (2 RKI1+/loxP-PTPI-RKI1 micron ori and URA-3) and E. coliRPE1+/loxP-PTPI-RPE1 (pBMR ori and ampicillin resistanceTKL+/loxP-PTPI-TKL delta::PTPI- gene: beta-lactam antibiotic). xylAPADH1-XKS::delta pMU624 also carries the T. emersonii (pMU782)fur1::nat;[pMU624] CBH1 + CBDTrCBH1 gene regulated by the ENO1 promoter andterminator. M0759 fur-1::hyg/fur-1::nat ura- M0867 The second copy ofthe genomic 3::kanMX/ura-3::kanMX FUR-1 gene was deleted andgre3::loxP/gre3::loxP TAL1+/loxP- replaced with a hygMX cassette. ThePTPI-TAL1 RKI1+/loxP-PTPI-RKI1 hygMX gene cassette encodes for aRPE1+/loxP-PTPI-RPE1 hygromycin B phosphotransferase TKL+/loxP-PTPI-TKLdelta::PTPI- that confers resistance to hygromycin xylA PADH1-XKS::deltaB (an aminoglycoside antibiotic). (pMU782) fur1::nat; [pMU624];(pMU1037) fur1::hyg M1088 fur-1::hyg/fur-1::nat ura- M0759 Two distinctintegration cassettes 3::kanMX/ura-3::kanMX were transformed into thestrain and gre3::loxP/gre3::loxP TAL1+/loxP- multiple copies wereintegrated into PTPI-TAL1 RKI1+/loxP-PTPI-RKI1 the genome at delta site.One RPE1+/loxP-PTPI-RPE1 cassette contained the cellulolyticTKL+/loxP-PTPI-TKL delta::PTPI- genes S. fibuligeria BGL and C.lucknowense xylA PADH1-XKS::delta [pMU624] CBH2b. The other (pMU1260)delta::PGKprom- cassette contained the cellulolytic SfBGL-PGKterm,ENO1prom- genes S. fibuligeria BGL and a T. emersonii TeCBH +TrCBD-ENO1term chimeric CBH1. (pMU1169) delta::PGKprom- SfBGL-PGKterm,ENO1prom- ClCBH2-ENO1term M0963 fur-1::hyg/fur-1::nat ura- M0759 LinearDNA from the 4 plasmids 3::kanMX/ura-3::kanMX shown was transformed intoM0759. gre3::loxP/gre3::loxP TAL1+/loxP- 24 of the resulting colonieswere then PTPI-TAL1 RKI1+/loxP-PTPI-RKI1 passaged for a week in YPDmedia RPE1+/loxP-PTPI-RPE1 containing zeocin at a low level (50 ug/mL),TKL+/loxP-PTPI-TKL delta::PTPI- and assayed. The resulting xylAPADH1-XKS::delta strain M0963 was the best of those (pMU782) fur1::nat;[pMU624]; found in the avicel assay. (pMU1037) fur1::hyg; (pMU755)delta::ZeoMX, ENO1prom-TeCBH1w/TrCBD- ENO1term; (pMU809) delta::ZeoMX,ENO1prom- ClCBH2b-ENO1term; (pMU663) delta::ZeoMX,ENO1prom-CfEG-ENO1term; (pMU864) delta::ZeoMX, ENO1prom-SfBGL-ENO1term

Example 16 Selection of an Endogluconase for Expression in a RobustXylose-Utilizing Strain

Endoglucanases augment the activity of cellobiohydrolases, andtherefore, the ability of family 5 endoglucanases to complement thepreviously identified CBH1 and CBH2 was invetigated. Five family 5endoglucanses were selected and cloned under control of the ENO1promoter/terminator using the pRDH122 expression plasmid as shown inTable 14.

TABLE 14 Family 5 endoglucanases expressed in S. cerevisiae. TheoreticalExpression enzyme Organism & Gene: CBM domain: plasmid: size Da*Aspergillus kawachii C-terminal CBM1 pRDH145 55034.58 egA Heteroderaschachtii C-terminal CBM2 pRDH146 43739.46 eng1 Hypocrea jecorinaN-terminal CBM1 pRDH147 44226.91 (anamorph: Trichoderma reesei) eg2Orpinomyces sp.PC-2 2x C-terminal pRDH148 53103.40 celB CBM10 Irpexlacteus en1 N-terminal CBM1 pRDH149 42357.15

All plasmids expressing the 5 new EG2-type cellulases were transformedto Y294 (a lab strain) and M0749 (robust xylose utilizing strain;described above) and transformants were confirmed via PCR. FIG. 28 showsseveral of the M0749 strains that were spotted on SC^(-URA) platescontaining 0.2% of either CMC or lichenin or barley-3-glucan. As can beseen in FIG. 28, the M0749 reference strain yielded small zones on theCMC containing plates. Both pMU471 (Coptotermes formosanus EG) andpRDH147 based strains yielded very good clearing zones on all the testedsubstrates.

Along with the reference strain and a strain expressing the Coptotermesformosanus EG (pMU471), the five eg2 expressing strains were tested foravicel and PASC hydrolysis while the cbh2 expressing strains were testedfor activity on avicel. The strains were grown in double strengthSC^(-URA) medium (3.4 g/L YNB; 3 g/L amino acid dropout pool withouturacil; 10 g/L ammonium sulfate; 20 g/L glucose) that was buffered to pH6 (20 g/L succinic acid; 12 g/L NaOH, set pH to 6 with NaOH). 10 mLCultures in 125 mL Erlenmeyer flasks were grown at 30° C. for threedays. Three flasks were inoculated for each strain. After incubation,samples were taken for gel analysis and activity measurement. Aftercentrifugation of the samples, 12 μl of each was taken, added to 5 μl ofprotein loading buffer and boiled for 5 minutes. The samples weresubsequently loaded on a 10% SDS-PAGE and separated, followed by silverstaining. The results are shown in FIG. 29. Not all strains producedvisible bands in the expected size range. The C.f.EG appeared as a bandof about 55 kDa as previously seen but the band produced by M0749 seemsto be slightly larger than the one produced by Y294. No bands werevisible for the H. schachtii eng1, Orpinomyces celB, or I. lacteus en1products. The H. jecorina EG2 produced by Y294 and M0749 was visible as˜57 kDa bands. The increased weight compared to the predicted 44 kDAsize may represent hyperglycosylation. The A. kawachii EGA produced byY294 was visible as a ˜42 kDa band. However, the A. kawachii EGAproduced by M0749 was clearly visible as a ˜120 kDa band. The extraweight may signify hyperglycosylation.

All strains were tested for activity using the high-throughput avicelconversion method as prescribed. Strains expressing endoglucanases werealso tested for activity on PASC. The DNS used for the assay procedurecontained phenol which, according to literature, renders greatersensitivity. Activity data can be seen in FIG. 30.

The M0749 strain expressing H.j.eg2 (pRDH147) produced the highestlevels of secreted activity as measured on PASC or avicel of the EG2stested. The activity of this enzyme was higher on PASC and avicel thanC.f.EG (pMU471). The synthetic A. k. EGA (pRDH145) also gave appreciableactivity on both substrates. This product seems to have been produced athigher levels in M0749 than in Y294 and yielded greater activity thanC.f.EG on avicel and PASC when produced in this strain.

Example 17 Expression of an Endogluconase in Robust Xylose-UtilizingYeast

Several strains were created to test the impact of co-expressing TrEG2with CBHs in a robust xylose utilizing strain background. M1088 wastransformed with a construct to integrate TrEG2 at the rDNA locus usingthe Sh-ble gene as a marker (pMU1409). A similar transformation wasdone, but integrating TeCBH1w/TrCBD to increase the copy number of thatgene. 43 transformants from both transformations along with duplicateM1088 cultures were grown in 20 ug/mL zeocin containing YPD and theavicel assay was performed. FIG. 31 shows the results of those assays.The data show that a very large proportion of strains transformed withthe TrEG2 construct had significantly increased avicel conversionability, while transformants with additional TeCBH1w/TrCBD copies hadonly marginal improvements in avicel hydrolysis.

Of the strains assayed, the top 9 candidates were chosen and restreakedfor single colonies. These single colonies were then grown in YPD with 2transfers to equal a total of 18 generations. The final transfer(passaged data in FIG. 32) was compared to the first YPD culture(original data in FIG. 32). The data confirms that there is an ˜50%increase in ability of the yeast supernatant to convert avicel whenTrEG2 is overexpressed.

In addition, strain M1403, which contains heterologous genes encoding S.fibuligera (SfBGL), cellobiohydrolase 2b from C. lucknowense (ClCBH2b),cellobiohydrolase I from T. emersonii fused to the T. reeseicellobiohydrolase I cellulose binding domain (TeCBH1+CBDTrCBH1), andHeterodera schachtii eng1 was produced in the M1254 background. StrainM1284, which contains heterologous genes encoding those same fourcellulases was produced in the M0509 background. Strains M1284 and M1403are described in more detail in Table 15.

TABLE 15 Endogluconase Expressing Yeast Strains. Strain Genotype ParentDescription M1403 (pMU1339) delta::MET3prom- M1254 Linear DNA cassettescreated by SfBGL-PGKterm, ENO1prom- restriction digests of plasmids wereTeCBH1 + TrCBD-ENO1term integrated in multiple copies into the (pMU1260)delta::PGKprom-SfBGL- genome at the Ty1 delta sites and PGKterm,ENO1prom- rDNA sites. TeCBH + TrCBD-ENO1term (pMU1169)delta::PGKprom-SfBGL- PGKterm, ENO1prom-ClCBH2- ENO1term (pMU1409)rDNA::ZeoMX, ENO1prom-HjEG2- ENO1term M0991 gre3::loxP/gre3::loxPTAL1+/loxP- M0509 A single copy of the genomic LEU-2 PTPI-TAL1RKI1+/loxP-PTPI-RKI1 gene was deleted and replaced with aRPE1+/loxP-PTPI-RPE1 hygMX cassette. TKL+/loxP-PTPI-TKL delta::PTPI-xylA PTPI-XKS LEU2/leu2D::hph M0992 gre3::loxP/gre3::loxP TAL1+/loxP-M0991 The second copy of the genomic PTPI-TAL1 RKI1+/loxP-PTPI-RKI1LEU-2 gene was deleted and RPE1+/loxP-PTPI-RPE1 replaced with aStreptomyces noursei TKL+/loxP-PTPI-TKL delta::PTPI- nat1 cassette. xylAPTPI-XKS leu2D::hph/ leu2D::nat M1162 gre3::loxP/gre3::loxP TAL1+/loxP-M0992 A linear DNA cassette created by PTPI-TAL1 RKI1+/loxP-PTPI-RKI1restriction digests of plasmid RPE1+/loxP-PTPI-RPE1 pMU1379 wasintegrated in multiple TKL+/loxP-PTPI-TKL delta::PTPI- copies into thegenome at the Ty1 xylA PTPI-XKS leu2D::hph/ delta sites. leu2D::nat(pMU1379) delta::leu2-19, ENO1prom-TeCBH + TrCBD- ENO1term M1284gre3::loxP/gre3::loxP TAL1+/loxP- M1162 Linear DNA cassettes created byPTPI-TAL1 RKI1+/loxP-PTPI-RKI1 restriction digests of plasmidsRPE1+/loxP-PTPI-RPE1 pMU1169 and pMU1409 were TKL+/loxP-PTPI-TKLdelta::PTPI- integrated in multiple copies into the xylA PTPI-XKSleu2D::hph/ genome at the Ty1 delta sites and leu2D::nat rDNA sites.(pMU1379) delta::leu2-19, ENO1prom-TeCBH + TrCBD- ENO1term (pMU1169)delta::PGKprom-SfBGL-PGKterm, ENO1prom-ClCBH2-ENO1term (pMU1409)rDNA::ZeoMX, ENO1prom-HjEG2-ENO1term

Example 18 Conversion of Lignocellulosic Substrates Via CBP YeastStrains

Expression of cellulases in yeast, particularly CBH1 (T. emersonii CBH1w/ T. reesei CBD attached), CBH2 (C. lucknowense CBH2b), EG2 (T. reeseiEG2), and BGL (S. fibuligera BGL) dramatically reduces the need forexternally added enzymes during enzymatic conversion of lignocelluloseto ethanol. To test the effect of overexpressing these enzymes, severalstrains were constructed and tested on a number of substrates.

FIG. 33 presents data from a CBP fermentation of paper sludge by anengineered thermotolerant S. cerevisiae host strain (parent strainM1254, cellulolytic derivative M1403). The data for M1254 alonedemonstrates that the addition of cellulase (i.e. zoomerase) is requiredfor ethanol production from paper sludge. The data for M1430 where noexternal cellulase is added (filled orange squares), demonstrates thatthis strain can convert a substantial fraction (˜80%) of the“convertible” substrate by virtue of its expressed cellulases.Fermentations with additional external cellulase added to the M1403strain demonstrate the ultimate potential of enzymatic conversion forthe paper sludge substrate. Visual inspections demonstrated that thenon-CBP strain was not able to liquefy the substrate, whereas the CBPstrain was.

Furthermore, the CBP strain M1179, which expresses CBH1, CBH2, EG2, andBGL can convert paper sludge to a large extent without added cellulaseenzyme. FIG. 34. The control strain in this reaction, M0509, made only asmall amount of ethanol during this reaction. The data also show thatM1179 can convert this material when loaded at lower cell density (1g/L) as opposed to the higher cell density (10 g/L) used in otherreactions. This implies that the strain is able to grow and producecellulase throughout the fermentation experiments.

Pretreated hardwood (PHW) can also be converted by CBP strains. FIG. 35,shows the effect of using a cellulase expressing strain (M0963),compared to a control strain not expressing cellulases (M0509) duringfermentation of PHW. The comparison demonstrates that the CBP strain canachieve the same yield of ethanol from PHW when only 2 mg/g of externalenzyme are loaded compared to when 4 mg/g of M0509 are loaded in theprocess. This 2-fold reduction in external enzyme needed represents alarge potential cost reduction in the process.

CBP strains are capable of producing high ethanol titers from PHW aswell. FIG. 36 shows that a 30% washed solids fermentation can generatetiters of ethanol up to about 70 g/L with minimal external enzyme loaded4 mg/g and a relatively low cell inoculum (2 g/L). The ability of thelow cell density cultivation to eventually catch up to and pass the highcell density culture indicates that the strain grows and continues tomake enzyme throughout the fermentation.

In addition to PHW, corn stover has been implicated as good substratefor conversion to ethanol via an enzymatic saccharification. FIG. 37demonstrates that pretreated corn stover can be converted well by CBPyeast strains. The CBP strain in this experiment was able to convertabout 82% of what was converted with a high enzyme loading (15 FPU, orabout 20 mg/g) could achieve. The non-CBP strain made about 60% of theethanol that the CBP strain was able to achieve.

Example 19 Comparison of CBH1 Cellulases

In order to provide additional data on the expression levels ofdifferent CBH1 enzymes, selected strains were grown in YPD-medium andactivities on MULac and Avicel were assayed. Both Y294 and M0749transformants were studied, and the results are shown in FIG. 38.

These examples illustrate possible embodiments of the present invention.While the invention has been particularly shown and described withreference to some embodiments thereof, it will be understood by thoseskilled in the art that they have been presented by way of example only,and not limitation, and various changes in form and details can be madetherein without departing from the spirit and scope of the invention.Thus, the breadth and scope of the present invention should not belimited by any of the above-described exemplary embodiments, but shouldbe defined only in accordance with the following claims and theirequivalents.

All documents cited herein, including journal articles or abstracts,published or corresponding U.S. or foreign patent applications, issuedor foreign patents, or any other documents, are each entirelyincorporated by reference herein, including all data, tables, figures,and text presented in the cited documents.

1-136. (canceled)
 137. A co-culture comprising at least two yeast hostcells wherein (a) at least one of the host cells comprises a firstheterologous polynucleotide comprising a nucleic acid which encodes acellulase which is an endoglucanase; (b) at least one of the host cellscomprises a second heterologous polynucleotide comprising a nucleic acidwhich encodes a cellulase which is a β-glucosidase; (c) at least one ofthe host cells comprises a third heterologous polynucleotide comprisinga nucleic acid which encodes a cellulase which is a cellobiohydrolase I(CBH1); (d) at least one of the host cells comprises a fourthheterologous polynucleotide comprising a nucleic acid which encodes acellulase which is a cellobiohydrolase II (CBH2); wherein the firstpolynucleotide, the second polynucleotide, the third polynucleotide andthe fourth polynucleotide are not in the same host cell; wherein theyeast host cells can grow at a temperature of at least 35° C. or above,wherein the endoclucanse, β-glucosidase, cellobiohydrolase I, andcellobiohydrolase II are secreted; and wherein the co-culture is capableof producing ethanol from Avicel. 138-149. (canceled)
 150. Theco-culture of claim 137, wherein at least one of the host cells is aSaccharomyces cerevisiae cell.
 151. The co-culture of claim 137, whereinat least one of the host cells is a thermotolerant host cell. 152-155.(canceled)
 156. The co-culture of claim 151, wherein the thermotoleranthost cell is a Issatchenkia orientalis, Pichia mississippiensis, Pichiamexicana, Pichia farinosa, Clavispora opuntiae, Clavispora lusitaniae,Candida mexicana, Hansenula polymorpha or Kluveryomyces host cell. 157.The co-culture of claim 156, wherein the thermotolerant host cell is aKluyveromyces host cell.
 158. (canceled)
 159. The co-culture of claim137, wherein said cellobiohydrolase I and cellobiohydrolase II areselected from the group consisting of a Humicola grisea CBH1, aThermoascus aurantiacus CBH1, a Talaromyces emersonii CBH1, aTrichoderma reesei CBH1, a Talaromyces emersonii CBH2, a Chrysosporiumlucknowense CBH2 and a Trichoderma reesei CBH2.
 160. The co-culture ofclaim 137, wherein said polynucleotide comprising a nucleic acid whichencodes a cellobiohydrolase I and cellobiohydrolase II, encodes a fusionprotein comprising a cellobiohydrolase and a cellulose binding module(CBM).
 161. The co-culture of claim 160, wherein the CBM is thecellulose binding module (CBM) of Trichoderma reesei Cbh2 comprisingamino acids of SEQ ID NO:28.
 162. The co-culture of claim 160, whereinthe CBM is the cellulose binding module (CBM) of Trichoderma reesei Cbh1comprising amino acids of SEQ ID NO:27 or Humicola grisea Cbh1comprising amino acids of SEQ ID NO:21.
 163. The co-culture of claim160, wherein the CBM is the cellulose binding module (CBM) ofChrysosporium lucknowense Cbh2b comprising amino acids of SEQ ID NO:25.164. The co-culture of claim 160, wherein the CBM is fused to saidcellobiohydrolase via a linker sequence.
 165. (canceled)
 166. Theco-culture of claim 137, wherein the cellobiohydrolase I and thecellobiohydrolase II are a Chrysosporium lucknowense cellobiohydrasecomprising the amino acids of SEQ ID NO:25 and a Talaromyces emersoniicellobiohydrolase comprising the amino acids of SEQ ID NO:23. 167-170.(canceled)
 171. The co-culture of claim 137, wherein the β-glucosidaseis a Saccharomycopsis fibuligera β-glucosidase comprising the amino acidsequence of SEQ ID NO:40. 172-173. (canceled)
 174. The co-culture ofclaim 137, wherein the endoglucanase is a Trichoderma reesei,Coptotermes lacteus, Coptotermes formosanus, Nasutitermes takasagoensis,Coptotermes acinaciformis, Mastotermes darwinensis, Nasutitermeswalkeri, Reticulitermes speratus, Aspergillus kawachii, Heteroderaschachtii, Hypocrea jecorina, Orpinomyces sp., or Irpex lacteusendoglucanase. 175-178. (canceled)
 179. The co-culture of claim 137,wherein: (a) said endoglucanase is Coptotermes formosanus endoglucanaseII comprising the amino acid sequence of SEQ ID NO:31; (b) saidβ-glucosidase is Saccharomycopsis fibuligera β-glucosidase I comprisingthe amino acid sequence of SEQ ID NO:40; (c) said firstcellobiohydrolase is Trichoderma emersonii cellobiohydrolase Icomprising the amino acids of SEQ ID NO:23; and (d) said secondcellobiohydrolase is Chrysosporium lucknowense cellobiohydrase IIcomprising the amino acids of SEQ ID NO:25.
 180. The co-culture of claim137, wherein: (a) said endoglucanase is Hypocrea jecorina endoglucanase2 comprising the amino acid sequence of SEQ ID NO:54; (b) saidβ-glucosidase is Saccharomycopsis fibuligera β-glucosidase I comprisingthe amino acid sequence of SEQ ID NO:40; (c) said firstcellobiohydrolase is Trichoderma emersonii cellobiohydrolase Icomprising the amino acids of SEQ ID NO:23; and (d) said secondcellobiohydrolase is Chrysosporium lucknowense cellobiohydrase IIcomprising the amino acids of SEQ ID NO:25. 181-183. (canceled)
 184. Theco-culture of claim 137, wherein at least one of the firstpolynucleotide, the second polynucleotide, the third polynucleotide andthe fourth polynucleotide is codon optimized.
 185. The co-culture ofclaim 137, wherein at least one host cell is a xylose-utilizing hostcell.
 186. The co-culture of claim 185, wherein the xylose-utilizinghost cell heterologously expresses Piromyces sp. E2 XyIA, overexpressesxylulokinase, ribulose 5-phosphate isomerase, ribulose 5-phophateepimerase, transketolase and transaldolase, and does not express theGRE3 gene encoding aldose reductase. 187-211. (canceled)
 212. Theco-culture of any one of claim 137, wherein the endoglucanase is aHumicola grisea, Thermoascus aurantiacus, Talaromyces emersonii,Trichoderma reesei, Coptotermes lacteus, Coptotermes formosanus,Nasutitermes takasagoensis, Coptotermes acinaciformis, Mastotermesdarwinensis, Nasutitermes walkeri, Saccharomycopsis fibuligera,Chrysosporium lucknowense, Reticulitermes speratus, Thermobfidafusca,Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui,Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromycesequii, Neocallimastix patricarum, Chaetomium thermophilum, Aspergillusterreus, Neurospora Crassa, Reticulitermes flavipes or Arabidopsisthaliana endoglucanase.
 213. The co-culture of any one of claim 137,wherein the cellobiohydrolase I is a Talaromyces emersoniicellobiohydrolase I comprising the amino acids of SEQ ID NO:
 23. 214.The co-culture of any one of claim 137, wherein the cellobiohydrolase IIis a Chrysosporium lucknowense cellobiohydrolase I comprising the aminoacids of SEQ ID NO:
 25. 215. The co-culture of any one of claim 137,wherein the endoglucanase is Trichoderma reesei comprising the aminoacids of SEQ ID NO:
 39. 216. The co-culture of claim 137, wherein: (a)said endoglucanase is Trichoderma reesei endoglucanase II comprising theamino acid sequence of SEQ ID NO:39; (b) said β-glucosidase isSaccharomycopsis fibuligera β-glucosidase I comprising the amino acidsequence of SEQ ID NO:40; (c) said first cellobiohydrolase isTrichoderma emersonii cellobiohydrolase I comprising the amino acids ofSEQ ID NO:23; and (d) said second cellobiohydrolase is Chrysosporiumlucknowense cellobiohydrase II comprising the amino acids of SEQ IDNO:25.